The expansion and intensification of agricultural lands (i.e., croplands and pasture areas) have become increasing threats to species diversity around the world. However, genus diversity should be considered for biodiversity conservation due to the important role that phylogenetic diversity and evolutionary history play shaping biodiversity patterns, particularly in the Neotropics, the most species-rich realm. Here, we explored agricultural land effects on distribution patterns of terrestrial vertebrate diversity at the genus level using cases from the Neotropics. We compiled distribution data on genera of amphibians, birds, mammals, and reptiles and explored the effects of agricultural lands on genus diversity distribution patterns for terrestrial vertebrates in the region using distribution modelling. Geography Weighting Regression (GWR) was used to explore the spatially variable relationship between agricultural lands and genus diversity. We found that there are significant, non-stationary relationships between agricultural lands and genus diversity in the Neotropics. The non-stationary relationship between croplands and genus diversity was stronger than that between pasture areas and genus diversity. Furthermore, these effects may depend on changes in genus groups (i.e., amphibians, birds, mammals, and reptiles) and biomes. The relationship was the strongest for the croplands and reptile diversity pair at the genus levels. The relationship between both croplands and pasture areas and reptile diversity was the largest in temperate broadleaf and mixed forests. Given the influence of crop and pasturelands on vertebrate distribution patterns, we argue that agriculture development should be considered in the spatial prioritization of conservation for vertebrates in the Neotropics. Agricultural lands should be used as environmental variables for distribution modelling, and understanding the impacts of agricultural lands on biodiversity is critical for effective conservation management in the Neotropics.