The amphibian fauna of Mesoamerica is one the most diverse, yet the most endangered in the area, perfectly exemplifying why the region is one of the world biodiversity hotspots. I carried out analyses from three interrelated perspectives: Conservation Genetics, species delimitation and Comparative Phylogeography of two genera of the family Hylidae in most of Mesoamerica: Agalychnis and Dendropsophus. First I performed a species delimitation analysis for the genus Agalychnis, with the specific aim of testing for cryptic diversity within the species A. callidryas, which exhibits wide morphological variation and the uncertainty of whether or not it represents more than one species has not been solved. Secondly, I did a conservation analysis of the genus Agalychnis adopting a comparative approach between endangered and non-endangered species and integrating ecological modelling and genetic information, with the aim of gathering key information for a better management and conservation planning at a regional scale of this genus in particular and Hylid frogs in general. This analysis resulted in the suggestion of short-term alternatives for conservation of critically endangered species and the management of non-endangered species at regional scale. Finally, I applied a comparative phylogeographic analysis between the two genera Agalychnis and Dendropsophus with the general objective of identifying factors and processes underlying species origin and dispersal within Mesoamerica. I proposed hypotheses for the colonization and dispersal of species of these two genera within Mesoamerica, on the basis of genetic data, geographical information, and ecological niche modelling. As part of data gathering for the latter analysis a new country record leading to the considerable extension of the geographical distribution of D. phlebodes is reported. The amphibian fauna of Mesoamerica is one the most diverse, yet the most endangered in the area, perfectly exemplifying why the region is one of the world biodiversity hotspots. I carried out analyses from three interrelated perspectives: Conservation Genetics, species delimitation and Comparative Phylogeography of two genera of the family Hylidae in most of Mesoamerica: Agalychnis and Dendropsophus. First I performed a species delimitation analysis for the genus Agalychnis, with the specific aim of testing for cryptic diversity within the species A. callidryas, which exhibits wide morphological variation and the uncertainty of whether or not it represents more than one species has not been solved. Secondly, I did a conservation analysis of the genus Agalychnis adopting a comparative approach between endangered and non-endangered species and integrating ecological modelling and genetic information, with the aim of gathering key information for a better management and conservation planning at a regional scale of this genus in particular and Hylid frogs in general. This analysis resulted in the suggestion of short-term alternatives for conservation of critically endangered species and the management of non-endangered species at regional scale. Finally, I applied a comparative phylogeographic analysis between the two genera Agalychnis and Dendropsophus with the general objective of identifying factors and processes underlying species origin and dispersal within Mesoamerica. I proposed hypotheses for the colonization and dispersal of species of these two genera within Mesoamerica, on the basis of genetic data, geographical information, and ecological niche modelling. As part of data gathering for the latter analysis a new country record leading to the considerable extension of the geographical distribution of D. phlebodes is reported.