Hypotheses of the historic biogeography of Neotropical anurans inhabiting lowland forests were generated using Parsimony Analysis of Endemicity. In order to establish comparisons with the biogeographical patterns of other vertebrates, previous cladistic analyses reported in the literature (for lizards and primates) were extended and reanalysed to match the geographical scope of the anuran analysis. Cladistic analysis of the distribution of 335 anuran species at 14 localities showed two regions that form a basal dichotomy: (1) Central America + Choco and (2) Amazon Basin + Brazilian Atlantic Forest. This result is interpreted as the first vicariance event that separated lowland Neotropical rainforests into Cis-Andean (east from the Andes) and Trans-Andean (west from the Andes) areas. Within the Cis-Andean localities, the earliest separation occurred between the Amazon Basin and the Brazilian Atlantic Forest. Within the Amazon Basin, three distinctive clusters are defined: (1) Belem, (2) Guianan Region, and (3) Upper Amazon Basin. Data sets on the distribution of anurans, lizards, and mammals have strong cladistic signal. Strong congruence exists among the area cladograms of anurans, lizards, and primates. All of them have, or at least did not conflict with: (1) a basal separation between Cis- and Trans-Andean regions, (2) a Central American clade, (3) the Choco Region is sister to the Central American clade, (4) an Amazon Basin clade, (5) an Upper Amazon Basin clade, and (6) a Guianan clade. The area cladograms are dichotomous and therefore do not support biogeographic theories that hypothesize simultaneous isolations of biotas in the Neotropics.