Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as taxonomy, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. In this study, we investigated the influence of taxonomy, sex, host size, locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal. We also analyzed the potential levels of microbial transmission between species that live in sympatry and syntopy. We studied Podarcis bocagei and Podarcis lusitanicus from northern Portugal (Moledo); and two invasive species, Podarcis siculus and Teira dugesii, and the native Podarcis virescens from Lisbon. We used a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Habitat/locality was found to be the main driver of the differences in composition and structure of gut bacterial communities of the studied lizards, with host effects more evident at finer taxonomic scales. Additionally, lizards from urbanized environments had higher microbiome diversity than lizards from rural areas. We detected a significant positive correlation between size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to higher exploratory behaviours. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota. These findings indicate that a diverse array of host and environmental factors can influence lizards gut microbiota.