Urban areas are primary causes of species' range fragmentation and reduction. However, relatively few studies have attempted to describe the habitat variables influencing the diversity and conservation of amphibians and reptiles, particularly in Mediterranean Europe and in large metropolitan areas. We explored this broad conservation ecology problem by studying the richness and diversity patterns in relation to a suite of six independent habitat variables in Rome, one of the most ancient cities of the world. We considered all the green remnant areas (n = 62) of Rome, ranging 1 to 41000 ha in size, which are interspersed within a sea of urbanized matrix. A total of 10 amphibian and 15 reptile species were studied. Their presence/absence patterns were assessed and the effects of the various habitat variables on each species were predicted by a logistic regression model. A total of 1261 presence records (404 amphibians and 857 reptiles) were analysed. Fragment size and wood size within each fragment did correlate significantly with the species richness of both amphibians and reptiles, and there was a clear threshold effect after 50 ha of wooded surface. The presence of water bodies positively affected the species distribution. One amphibian and three reptiles inhabited exclusively fragments 450 ha. The distance from the centre did not affect fragment species richness. The presence of most species of both amphibians and reptiles was positively influenced by the irregular versus circular shape of the wooded area. The legal protection of a given area did not influence the observed patterns but the total number of sheltered species. Overall, our study suggests that, in order to maintain the current diversity and population viability, it is necessary, in addition to water bodies' maintenance, to (1) preserve the wooded landscapes over 50 ha; (2) promote irregularly shaped increases in the wood surface; (3) maintain ecotonal boundaries.