Psychrophiles and hyperthermophiles
While on Earth, the majority of hyperthermophiles are archae, there is no reason sufficient evolution in another environment wouldn't result in humanoid hyperthermophiles. If one species is a psychrophile, it could easily survive in sub-zero temperatures, but will die within seconds, or instantly, if the temperature gets above -10 C. The other species, a hyperthermophile, can survive in extremely high temperatures, and anything under 100 C will kill them. There is no overlap in survivable temperatures, no common ground on which they can meet.
There are some organisms that feed on ionizing radiation. There are other organisms that produce enzymes which use ionizing radiation to repair damage (such as the enzyme photolyase). If one species evolves in an environment with such extreme radiation that blocking the radiation is impossible, then they may very well end up depending on that radiation for whatever reason (or perhaps they generate it themselves, and instead of filling themselves with lipids in fat as we do, they fill themselves with radon). The other species simply has to have evolved in an environment with extremely little radiation, far less than we are exposed to. They would evolve with very few, or no, biological mechanisms to repair genetic damage caused by radiation. Each species would die quickly in the other's environment.
Electric eels can create lethal currents to incapacitate or kill potential predators and prey. They are able to regulate the amount of electricity they produce, but this is not limited by physics. If a species were to generate high levels of electricity under nominal conditions (whether as a byproduct of their metabolism, an evolutionary protection mechanism, or any other reason), then it could be lethal for a different species to touch it. This could be extended to making close proximity lethal by having the other species highly sensitive to magnetic fields, e.g. by evolving with similar properties to modern electronics. Perhaps both species are cyborgs, where one of them produces a powerful electric field in order to function due to having evolved in conditions where extremely high power outputs are required, and the other is extremely sensitive to electric fields, as they could crash its internal vital components. If this species evolved in an environment where power conservation was vital, they would be using low-power components that are especially vulnerable to this.
Byproducts of metabolism
Cyanogenic bacteria are microorganisms that produce cyanide (CN-). This is extremely lethal to us, because it jams our vital metabolic machinery. If one humanoid evolved to produce high levels of a toxic gas (and had to get rid of it rapidly, preventing them from simply "holding it in"), they could not get anywhere near another humanoid species without killing it. If a cyanogenic organism our size were even in the same building as a human, we would die before even being able to escape. You could make it impossible for one species to even get close enough to touch the other by having each produce a mutually lethal gas, as they would mutually kill each other before getting close enough to touch.
Modern tanks are coated with so-called explosive-reactive armor. This is a type of armor which explodes violently outward if it is punctured or hit, with the goal being to deflect, melt, or decelerate anti-tank projectiles. If one species had skin coated in a chemical that reacts violently when in contact with a chemical that coats the other creature's skin, physical contact would be impossible, as it would result in both creatures being blown away from each other, and possibly killed. Since you did say they have to be on the same planet, this can't be something as extreme as matter vs antimatter, as they could not coexist at any significant level on the same planet.
Symbiotic relationships are common in nature. Imagine a scenario where one humanoid is surrounded by a symbiotic insect that protects and nourishes them, but would attack and kill the other species. It would be impossible for one species to get even close to the other without one of them dying, and it could very well be impossible to even temporarily get rid of the insects if their relationship involves obligatory symbiosis.