Agriculture poses a threat upon wildlife worldwide and particularly to reptiles. However, the effects of many crop types on reptile diversity remain unknown. In this field study, we examined the local effects of two understudied common crop types in Mediterranean regions, intensively cultivated vineyards and intensified-traditional olive plantations, on reptile diversity patterns. We compared measurements of diversity among an array of study plots representing each crop as well as plots in adjacent patches of natural habitat. We developed a new index, the Average Specialization Index, in order to compare the degree of habitat-specialization of the species in the different habitats. Among the habitat types examined, the natural patches were the most structurally heterogeneous and contained the greatest species richness and diversity. In contrast, the intensive vineyards were structurally homogeneous and were uninhabitable areas for reptiles. The more-traditionally cultivated olive plantations were intermediately heterogeneous and provided a unique habitat occupied by a community with a high proportion of reptile species considered to be habitat specialists. Despite showing high abundance and eveness, the reptile community within the olive plantations still contained a lower species richness and diversity compared to natural patches. In light of our results, we recommend implementing a more wildlife-friendly management strategy in landscapes converted to agricultural cultivation.