Racism can be seen most prominently in how the doctor treats Kino. The doctor is part of the racial elite; as such, he looks down on indigenous people like Kino, seeing them as racially inferior. That explains why the doctor sets out to cheat Kino out of his valuable pearl instead of giving him a fair price for it. The doctor doesn't think it right that someone he regards as his social and racial inferior should have more money or be able to enjoy a better lifestyle than himself. So he and his thugs do everything that they can to get their greedy hands on Kino's pearl without giving him anything like adequate compensation for his trouble.
Earlier in the story, the doctor had refused to treat Kino's son, Coyotito, even though he was seriously ill. Once again, we could see this as an example of racism. The doctor clearly doesn't believe that those of a supposedly lesser race deserve the same level of medical treatment as anyone else. He's only interested in patients who can pay their medical bills, and that immediately rules out the indigenous people.