<p>The rapid growth and expansion of Neotropical cities make it increasingly challenging to identify and delineate regions within the urban continuum, such as peri-urban and intra-urban regions, where transitional spaces, or ecotones, often function as biological filters. Despite their ecological importance, such zones remain underexplored within the urban contexts. In this study, we focused on bird communities to identify ecologically relevant regions within the urban continuum of a Neotropical city in southern Mexico (Tuxtla Gutiérrez, Chiapas). We assessed changes in avian community composition, species richness and phylogenetic diversity across peri-urban and intra-urban sites at increasing categorical distances from the urban center. Composition analysis revealed that bird distribution along the urban continuum is not uniform, showing greater species turnover than nestedness among areas, supporting the ecological distinction between intra-urban and peri-urban regions. Rarefied species richness was higher in the peri-urban region than in the intra-urban region, but differences were not statistically significant. Phylogenetic diversity was significantly higher in the peri-urban region, possibly due to unique, evolutionarily ancient species that are distantly related, contribute to greater phylogenetic differentiation and making it the key ecological distinction between regions. Our findings highlight the importance of identifying and managing ecologically distinct urban regions to support sensitive species and mitigate the impacts of urban expansion. Likewise, incorporating measures of diversity, such as phylogenetic diversity, along with spatial data, were effective in preserving key aspects of biodiversity, as it enables a more comprehensive understanding of species distribution and conservation priorities within urban landscapes.</p>