The spiny lobster Panulirus argus is an important benthic mesopredator and a major fishing resource across the Wider Caribbean region. This species is host to the pathogenic virus PaV1 and metacercariae of Cymatocarpus solearis, a digenean trematode whose first intermediate host remains unknown. Previous studies found that the probability of infection with PaV1 was higher in juvenile lobsters and in densely vegetated habitats (suggesting that marine vegetation can be an environmental reservoir for PaV1), whereas the probability of infection with C. solearis was higher for larger lobsters and in poorly vegetated habitats. To increase insight into the role of habitat and body size in the ecology of lobster diseases, the presence of both C. solearis and PaV1 in P. argus was investigated across three contrasting zones in Bahía de la Ascensión, Mexico (19°35′27″N, 87°38′06″W): reef, lagoon and shallow habitat. Additionally, habitat complexity, cover of benthic components, and macroinvertebrate biodiversity were characterized in each zone. Consistent with previous studies, probability of infection with PaV1 (both at a clinical and infective level) decreased with increasing lobster size and was highest in the seagrass-rich lagoon, supporting the idea that marine vegetation could be an environmental reservoir for PaV1. In contrast, the probability of infection with C. solearis increased significantly with lobster size but did not vary with zone, suggesting no relationship with benthic substrate type. However, based on results of macroinvertebrate diversity, the gastropods Cerithium litteratum and Tegula fasciata are put forward as potential candidates for the first intermediate hosts of C. solearis.