I see no reason they should be (they come from different planets), but if so, how can they have children?
Anakin is human.
“To be angry is to be human,” Padmé assured him.
“To control your anger is to be a Jedi,” Anakin was quick to reply, and he pulled away from her and stood up, turning to face the open door and the desert beyond.
Padmé was right there beside him, draping her arms about him. “Shhh,” she said softly. She kissed him gently on the cheek. “You’re human.”
- Star Wars: Attack of the Clones: Official Novelisation
And so is Padmé:
Armies … Jar Jar had spoken of armies. He seemed sure that his people would fight. Perhaps if the Humans of Naboo had cooperated more with the Gungans, the Trade Federation’s invasion would not have succeeded so quickly and easily. Perhaps even now, if they all cooperated … But that would mean starting a real war. The Trade Federation invaded us. Talking and diplomacy haven’t helped. Sometimes … sometimes you just have to fight back.
It therefore makes perfect sense that they can interbreed since humans are pretty common in the Star Wars universe.
Frankly, what makes far less sense is why someone like Padmé would fall for such a whiny man-child as Anakin, but that's a whole 'nother question.
Humans were a very ubiquitous species in the Star Wars universe. Although Anakin and Padme may have had different planets of origin, they were both human; humans could be found almost everywhere, and were the most numerous of species. (Don't confuse the individual's planet of origin with the SPECIES planet of origin, which, in the case of humans, was unknown; they had been around for a LONG time, by the time of the movies.)
The other answers have pointed out that Anakin and Padme are the same species (@Richard's answer has a nice proof) since it's possible for humans to come from different planets in a galaxy where interstellar travel is ubiquitous and relatively cheap.
However, more can be said to address your sub-question:
how can they have children?
The assumption here is that individuals from different species cannot procreate with each other. Or, perhaps, that individuals on their respective home planets had genetically diverged due to lack of cross-breeding and that Anakin and Padme may not be able to mate for that reason.
However, within the Star Wars universe it is actually possible for humans to mate with certain Near-Humans. The resulting offspring is called a hybrid (though, to the best of my knowledge, it has never been explained exactly how such mating is possible). For example, according to the article "Everything You Always Wanted to Know about the Nightsisters but Were Afraid to Ask" (written by Leland Chee) the Dathomirians are an entire hybrid race resulting from human females mating with male Zabraks.
Thus, even if Anakin and Padme were members of different human/Near-Human species or their ancestors had genetically diverged, it would be possible in the Star Wars universe for them to procreate.
All humans from Star Wars likely originated from Coriscant (or however you spell that planet). They're obviously the same species. It's likely that the humans had spaceships. Duh! So several thousand years later, when we've colonized Mars and a cloud city on Jupiter, we're still going to be human, even those who'd never seen earth in generations. In star wars, it works the same way.