An example that comes to mind is sexism. On the one hand, men and women are equal, but on the other they most certainly are not interchangeable. Women require their own bathrooms not only because of modesty but because apparently men's restrooms get too dirty. Men's restrooms, on the other hand, often have urinals, which are not useful to women. Because of these and many more differences between men and women, the sexes have been segregated throughout history, and this has caused a fair deal of hatred and inequality. A culture may not always be racist, but I can't think of many that aren't sexist.
Thus, from this example, I would suggest that hatred and bigotry can exist in as many forms as there are differences between intelligent individuals. It may be important to note that hatred weakens by necessity; that is, I suggest that sexism has never reached the evils of racism because men and women need each other. Similarly, I've heard the argument that American slave owners were not nearly as 'racist' as their Northern cousins; the slaves were their property, not their competitors, thus there was no reason to hate them.
So I would say that the level of hatred between two groups is proportional to the threat or benefit they provide. If humans are at war with these species, they will hate them; on the other hand, if they harvest them for their pelts and meat, then they should be treated more nicely, if not more equally.
As for specism, though, there are differences between your species (and their respective races, for that matter); denying that would be stupid. So specism will be logical, and thus probably won't be going away like racism is, though people might find ways to be nicer about it.