Caridean shrimp are critical components of sea-grass communities and occasionally harbor parasitic bopyrid isopods, which can negatively impact their hosts. However, the ecological factors that drive infection rates of parasitic bopyrid isopods in host carideans are poorly known. We examined 43,875 carideans belonging to 6 families and 11 genera from 19 shallow-water localities throughout south Florida. Of these, only 114 shrimp (belonging to 5 genera) were found to be infested with bopyrids (an additional 251 had deformed carapaces consistent with recent infestation). We identified 13 bopyrid species (Bopyrina abbreviata, Bopyrinella thorii, Eophrixus subcaudalis, Loki circumsaltanus, Metaphrixus carolii, Ovobopyrus alphezemiotes, Parabopyrella lata, Parabopyrella richardsonae, Parabopyriscus stellatus, Capitetragonia alphei, Probopyrus pandalicola, Schizobopyrina urocaridis, and an unidentified Diplophryxus sp.). Bopyrid infection rates were very low throughout the study area, with mean prevalence of 0.26% (range 0.04–1.48%). Furthermore, each isopod species was only ever recovered from a single host genus, suggesting a high degree of genus-level specificity. At the community level, multivariate analyses (RELATE and BVSTEP) indicated that bopyrid community composition was correlated with host community structure, latitude, and temperature, as well as the relative coverage of the sea grasses Thalassia sp. and Syringodium sp. and the alga Penicillus sp. Only 4 parasite taxa were sufficiently abundant to warrant further analysis at the individual taxon level: B. abbreviata, B. thorii, Diplophryxus sp., and P. pandalicola; stepwise regression indicated that bopyrid infection rates were primarily driven by the abundance of their specific hosts, and secondarily by environmental variables such as temperature and depth, as well as algal and sea-grass community composition.