Biodiversity has been proposed as a major ecological factor determining disease prevalence and emergence. However, the relationship between biodiversity and disease risk remains underexplored. Few studies focus on host-virus systems and, particularly on plant viruses. To address this subject, the prevalence of virus infection and disease symptoms was monitored in wild-pepper (chiltepin) populations under different levels of human management. For these populations, species diversity, host genetic diversity and plant density were determined. Higher levels of human management resulted in increased disease risk, which was associated with decreased habitat species diversity and host genetic diversity, and with increased host plant density. More specifically, for all and for wild chiltepin populations, species diversity of the habitat was the primary predictor of disease risk; and host genetic diversity was the primary predictor in managed populations, with host density being always a poorer predictor of disease risk. These results support a dilution effect of biodiversity on disease risk, and underline the relevance of different ecological factors in determining disease risk in wild and in human-managed habitats.