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A hypothesis of historical area relationships for Mexico, Central, and South America was investigated by a cladistic biogographic analysis using 10 taxon cladograms of the herpetofauna of Mexico. A hypothesis is presented based on previous narrative biogeographic scenarios and compared with the general area cladograms (GACs) obtained using reconciled trees of COMPONENT 2.0 and Brooks Parsimony Analysis (BPA). For tree reconciliation, 1 000 trees were saved after the analysis. BPA yielded 18 GACs (CI = 0.805, RI = 0.549). The GAC derived from tree reconciliation is more or less pectinate and has only 3 groups of 2 areas each. These groups consist of the Chihuahuan and Sonoran deserts as sister areas on the one hand (DCHI, DSON), and the Sierra Madre Oriental and Occidental as sister areas oil the other (SMOR, SMOC). This latter clade is sister to the Chihuahuan and Sonoran desert clade. The third group has the Transvolcanic Belt and Sierra Madre del Sur as sister areas (TVA, SMEX). The GAC obtained by BPA showed 4 main groups of areas: the first is comprised of the Pacific coast of Mexico and the Balsas Depression (PCBAL), the Sierra Madre del Sur (SMEX), and the Transvolcanic Belt (TVA); the second group includes the Sierra Madre Oriental (SMOR), Sierra Madre Occidental (SMOC), Sonoran (DSON) and Chihuahuan deserts (DCHI) the third comprised the Highlands of Chiapas and Guatemala (CHIG), the Eastern Lowlands, on the Atlantic coast (ELL) and the Semiarid Lands of Tamaulipas-Texas (TAMS); the fourth group contains the Western Lowlands, in the Pacific coast (WLL) and northern South America (SA); the Talamanca Ridge (TALA) is isolated at the base of the 3 first groups. The GAC from narrative biogeography contains 3 groups: the first has areas of northern Mexico (DSON, DCHI, TAMPS), the second has areas from central Mexico (PCBAL, SMOR, SMOC, TVA), and third has areas from southern Mexico and Central America (SMEX, CHIG, TALA, WLL, ELL, SA). In general, the GAC from the BPA analysis shared more groups with the hypothesis of narrative biogeography; when compared to the GAC obtained via reconciled trees; however, all the GACs obtained are topologically distinct. Accounting for the lack of congruence between the narrative biogeography GAC, reconciled tree analysis and BPA, is challenging due to several factors: 1), erroneous interpretation of vicariant events when constructing the narrative area cladogram; 2), lack of congruence among patterns of speciation and endemism for the taxa used in this analysis; 3), the region under study is a geologically complex zone and the history of the inhabiting biota is equally complex: 4). there are many widespread species present in this region, and may obscure the relationship among the areas of endemism: 5), the patterns of endemicity are poorly-defined and -studied in Mexico and Central America 6), the incorrect selection of the areas of endemism used in this study. Despite these issues the results presented here are evidence of the multi-dimensional complexity of historical biogeographical processes in the region.