Black abalone Haliotis cracherodii from California, USA, and Baja California, Mexico, have faced massive population declines for more than 30 yr. The main factors contributing to these declines have been overfishing, pollution, climate change, and lethal diseases, such as withering syndrome, caused by the intracellular bacterium Candidatus Xenohaliotis californiensis (CXc). In recent years, the presence of an associated bacteriophage, pCXc, infecting CXc was detected and reported in some abalone species from California and Baja California. In the present study, 199 black abalone fecal samples from 14 sites along the Baja California coast were analyzed for the presence of CXc and pCXc DNA. The overall prevalence of bacteria and phage-infected bacteria was 44 and 38%, respectively. We found significant differences in the relationship between the prevalence and the mean lengths of abalone throughout the study area. This result is probably due to differences in the size-frequency distribution between sampling zones. The only site where we found a relationship between prevalence and length was in Isla Todos Santos. We did not see a relationship between abalone density and the prevalence of the bacteria and the phage. Additionally, we found a positive but non-significant correlation in prevalence between CXc and pCXc. This study is the first to detect the presence of pCXc DNA in wild populations of black abalone of Baja California.