I contrast mitochondrial DNA genealogies based on 612 bp of the cytochrome b gene across four co-distributed species of frogs in Northeastern Brazil. They are Hyla albomarginata, Hyla branneri, Proceratophrys boiei, and Scinax nebulosus. Samples were collected from the core or edge of six rainforest remnants in the states of Pernambuco and Alagoas. Three fragments are located within the humid Atlantic Forest morphoclimatic domain (municipalities of Cabo de Santo Agostinho, Ibateguara, and Jaqueira), two are located in the transition zone between the Atlantic Forest domain and the semi-arid Caatinga (Caruaru and Timbaúba), and one is found within the Caatinga (Brejo da Madre de Deus). Results show that local patterns and levels of genetic diversity are influenced by taxon-specific habitat requirements. Populations of the montane, closed-canopy species P. boiei show strong geographical structure, reflecting barriers to gene flow that predate human-driven habitat destruction. Species occurring along forest edges, such as H. albomarginata and S. nebulosus, show genetic patterns similar to those of P. boiei, but lower levels of genetic divergence. The more generalist Hyla branneri shows no geographic pattern. The data are in agreement with distribution and fossil data gathered for other groups of organisms, suggesting that mesic forests occupied the currently arid Caatinga in the recent past.