Peninsular bighorn sheep (Ovis canadensis nelsoni) are found exclusively in Southern California and Baja Mexico. They are federally endangered due to multiple threats, including introduced infectious disease. From 1981 - 2017, we conducted surveillance for 16 pathogens and estimated population sizes, adult survival, and lamb survival. We used mixed effects regression models to assess disease patterns at the individual and population levels. Pathogen infection/exposure prevalence varied both spatially and temporally. Our findings indicate that the primary predictor of individual pathogen infection/exposure was the region in which an animal was captured, implying that transmission is driven by local ecological or behavioral factors. Higher Mycoplasma ovipneumoniae seropositivity was associated with lower lamb survival, consistent with lambs having high rates of pneumonia-associated mortality, which may be slowing population recovery. There was no association between M. ovipneumoniae and adult survival. Adult survival was positively associated with population size and parainfluenza-3 virus seroprevalence in the same year, and orf virus seroprevalence in the previous year. Peninsular bighorn sheep are recovering from small population sizes in a habitat of environmental extremes, compounded by infectious disease. Our research can help inform future pathogen surveillance and population monitoring for the long-term conservation of this population.