Metagenomic sequencing was undertaken to identify unknown pathogens affecting sharks of San Francisco Bay. The sequences in this project derive from cerebrospinal fluid of shark species including Leopard Shark (Triakis semifasciata), Great White Shark (Carcharodon carcharias), Soupfin Shark (Galeorhinus galeus), Pacific Angelshark (Squatina californica), and Sevengill Shark (Notorynchus cepedianus). Sequences of a potential pathogen, the ciliate Miamiensis avidus, were identified in these data.