Coyote Creek has historically, and still does support the most diverse fish fauna among the Santa Clara Valley Basin watersheds. It supports 10 to 11 native fish species out of the original 18. Species known to occur currently include Pacific lamprey ("Lampetra tridentata"), steelhead/resident rainbow trout ("Oncorhynchus mykiss"), chinook salmon ("Oncorhynchus tshawytscha"), California roach, Hitch ("Lavinia exilicauda"), Sacramento blackfish ("Orthodon microlepidotus"), Sacramento pikeminnow, Sacramento sucker, three-spined stickleback, prickly sculpin ("Cottus asper"), riffle sculpin ("Cottus gulosus"), staghorn sculpin, and tule perch ("Hysterocarpus traskii"). Three species, the thicktail chub, splittail, and Sacramento perch have been extirpated from the drainage; the thicktail chub is extinct.