Crop area (CA) and agricultural management intensity (AMI) are the two main factors associated with agricultural systems that can negatively affect the diversity of animal communities. Despite existing knowledge, the effect of both factors has not been analyzed for all biological groups. In this study, we evaluated the effect of CA and AMI in two types of crop farming (intensive and semitraditional) on the diversity of tropical lizards in a mosaic of agricultural land and subdeciduous tropical forest. The results of this study show that by grouping crops, CA reduces lizard species richness and diversity, while lizard abundance is not related to either CA or AMI. However, when crops are assessed separately, AMI and CA are found to reduce richness and diversity in semitraditional crops. Lizard abundances in both types of crops are unrelated to any factor. Our results show that lizard diversity is more affected by CA than AMI; however, the magnitude of the effect depends on the type of crop farming.