TL/DR: Not after a 'mere' 500,000 years. In fact we should know that the other humans came from earth, if not what type of earth animal they evolved from, even if there were half a billion years or more since we diverged from them.
Horsing around a little bit
To give a timeframe for comparison the last common ancestor of all equines (which comprise horses, donkeys, zebra etc) was about 4.1 MYA (million years ago). That's nearly ten times the length of time you suggested.
Looking at equines they look similar. You can guess if a species is equine just by looking at it even if no one told you. After all you probably were never explicitly told a zebra was an equine, you just looked at it and knew. That's because 4 MYA isn't enough time for a species to evolve into something truly foreign. Any species that is split by only 4-5 MYA would look close enough that anyone familiar with evolution would naturally presume they had a close common ancestor. Many equines can also usually interbreed to some degree, though their children are usually infertile, so humans split by 4 MYA likely could interbreed at least occasionally.
Now on the one hand you could argue that entirely different worlds would create such a hugely different environment as to encourage rapid evolutionary change. To this I'd say that's true, if it wasn't for humans technology.
As it is we won't adapt to our environment, we will adapt our environment to us. Were going to pick worlds that are 'earth like' and use technology to make the worlds more earth like. There may be some minor difference our technology can't adjust for, gravity being the biggest one we would struggle to change, which may be a driver for evolution but most of the potential drivers will be compensated for by technology. In fact I believe humans on different worlds will be far less likely to evolve into different forms then ancient equines, due to our technology.
Technology > evolution
Species living in stable environments don't change, look at alligators which have stayed roughly the same since the time of dinosaurs! If a certain form is working for your environment then there isn't much incentive to try out new adaptation and koinophilia - the instinctual avoidance of things that are different, like novel mutations, in mates - will result in the species staying mostly unchanged. You need some sort of change in your environment, some massive pressure pushing a species to need to adapt, for major changes to be likely to happen 'rapidly' - and yes 5 MYA is rapid from an evolutionary perspective. Now I definitely do not expect human's environment to stay static. However, I do expect the exact opposite, our environment will change so rapidly, due to technology, that no one mutation will be favored long enough to spread through the population before the environment and pressures change again, which will ironically result to the same effect of humans staying somewhat static evolutionarily much as alligators have.
Look at our technology 2000 years ago vs today, it's utterly different and yet 2,000 years is a blink in the eye from an evolutionary perspective. This means that technology is going to change faster then our species can adapt. As new technologies come about new evolutionary pressures will as well. For example right now car accidents are a major cause of death in first world nations. This means currently there is a fairly strong evolutionary pressure to evolve to be able to process movement at high speeds and make the the sort of rapid decision required to avoid accidents. However it will be no more then a generation or so before self driving cars likely take over and the need to be good at driving disappears. The few generation between when cars became common and when we no longer drove them were not enough for natural selection to significantly change humans to make us better at driving. The same patter will happen with new technologies, they will change so fast that evolution can't 'keep up' and since the exact pressures put on humans to survive will constantly change with our technology there will not be any one mutation favored long enough to permeate through a population. In absence of a long lasting evolutionary pressure favoring adaptation humans will default to persisting their current form.
There is no such thing as humanoid aliens
Honestly given how utterly foreign any species evolved entirely on a different would should be if we go to another planet and find anything remotely mammal like the only logical conclusion would be it likely came from earth. If your humans know that other humans traveled to other worlds and they run into any creature on another world that is carbon based with four limbs and eyes, no matter how bizarre it's appearance otherwise, the only remotely plausible explanation for such similarity to earth animals is it's from Earth origin. The only real question would be what earth animal this one originally evolved from. Of course that means DNA tests would happen almost immediately and our exact common ancestor being identified via DNA in less then a few years of meeting each other. This is true even after hundreds of millions of years when all the humans look utterly different.
How many billons of years can we cut that timeline down to?
If you want there to be any noticeable change in your human species you need to cut back on technology so more stable evolutionary pressures can encourage adaptations. If humans lost their advanced technology, possible due to disasters after landing preventing them from building the infrastructure necessary to support it, then a species reverting to swords and sandals level technology will defiantly struggle with the utterly foreign world they are living in and likely adapt to better survive it. If both of the human subspecies regressed technologically and had to rediscover their technology then their evolving to look different is far more likely since technology isn't favoring stability of form, though again not nearly enough for a mere 5 MYA to make them truly foreign.
If you take that further and presume your human species no longer remembers they originated on another world, and thinks space travel only recently became possible for species on their world, the likely hood that animals from another world came from the same common decent as them would seem much lower. I mean how likely would you buy an argument that dinosaurs built spaceships and now live on another world if I told you that since the creatures we just found on alpha centauri have eyes they must have come from something like dinosaurs?
If you make one of these two human subspecies non-sapient you would further make it seem implausible they built spaceships and flew to another world, and make the divide between the two human subspecies seem far more vast since humanity tends to define itself by it's sapience.
(Here I should mention that it seems unlikely human technology would regress this much and humans still survive, as any planet humans travel to would likely be so foreign that without a relatively high degree of technology to help us adapt we couldn't survive on the world. The idea of evolving towards loosing sapience, and such a non sapient species still surviving on a foreign world, seems particularly implausible without either billions of years of time for us to adapt to the world or this new world being far more earth like then is realistic. However, you get some poetic license here; few are going to notice and nitpick on something that trivial so I say go ahead and have technology regress if it serves your story)
So my suggestion would be both groups lost technology, one group's technology was so lost that they eventually became non-sapient. Then when your one sapient species finds another non-sapient species that looks like them; but their certain didn't come from their home world - which they think of as being the one they live on now not Earth - they would be less likely to guess they came from a the same species originating on another world.
Of course the utterly implausibility of two alien species sharing so many similarities as any of our decedents would share should still lead to experts asking allot of questions. DNA tests would still be expected to happen almost immediately, and DNA comparisons would be made. The plausibility of the two human subspecies sharing a common ancestor would still be known from fairly early on. The only real issue would be convincing people of how that happened when everyone would be making the equivalent of "dinosaurs couldn't build spaceships" argument.
You would instead get the sapient humans arguing the DNA evidence is wrong because it shows our last common ancestor as happening before humans even evolved on their home world! at that point evolutionary experts will point out that we always knew there was an unexplained lack of fossil records, or any other records, of animals earlier then whenever humans first touched down on their home planet and suggest maybe these creatures are somehow connected to that pre fossil record time period and may answer some of the huge questions as to why earth-like animals seemed to appear out of no were X million years ago. At that point things probably get political with religious leaders complaining that's heresy since everyone knows god created earth-like animals on their world back then and how dare you suggest otherwise etc etc. Eventually scientists will realize the non-sapient humans from the other world have a fossil record that dates back to, but no farther then, same time period as theirs. Then we get even more interesting questions about how two similar species mysteriously appeared on two worlds lightyears away at the exact same time. I imagine the standard arguments would boil down to 'god did it' and 'aliens did it'.
Of course this still requires a time period measured in hundreds of millions of years - tens of millions of years at minimum even if you push things- not thousands. Even then the possibility of common ancestry will come up almost immediately. The only real mystery would be how that common ancestor could exist given what the humans know of their own history.
