Urbanization involves the conversion of natural habitats into human-modified ecosystems and is known to reduce the diversity and abundance of indigenous plant and animal communities. Urbanization may lead to the extinction of indigenous species or facilitate the establishment of non-indigenous communities in cities and towns. We analysed sighting records held in wildlife databases to infer the probability of persistence of reptiles and amphibians (‘herpetofauna’) within Melbourne, Victoria, Australia. Throughout greater Melbourne, 81% (13) of the 16 frog species recorded had ≥95% probability of being extant in 2006, compared with 56% (22) of the 39 species of reptiles recorded. The number of frog species that had ≥95% probability of being extant in inner local government areas (LGAs) within 10 km of the centre of Melbourne was higher (86%) than in the outer LGAs (69%). Conversely, only 46% of reptile species had ≥95% probability of being extant in inner and outer LGAs. The proportion of reptile species with <50% probability of being extant in inner LGAs was higher than for frog species (25% and 7%, respectively), suggesting that reptiles have been negatively affected by urbanization to a much greater extent than frogs. Based on the probability of species being extant, frogs and reptiles exhibited variations in their response to urbanization between species that persisted (urban-adapters) and species that did not (urban-sensitive or urban-avoiders). These differences in response were likely related to individual species' life-history and their requirements for habitat, space and dispersal. To conserve herpetofauna in urban areas we need to maintain structural complexity in remnant habitat patches, and implement strategic policies and management actions that protect habitat remnants and habitat corridors.