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Fish communities of tropical lakes are commonly predicted by local environmental variables, including depth, temperature, oxygen concentration, and substrate composition. Increasingly, however, lacustrine fish communities are being impacted by invasive species. In the state of Quintana Roo, on the Caribbean versant of the Yucatan Peninsula in Mexico, inland aquaculture production has resulted in the widespread establishment of African tilapia (Oreochromis sp.). However, there are still limited quantitative data on their abundance relative to indigenous species, or their influence on native fish diversity. Here, we quantified the ichthyofauna of six lakes from this region, alongside physical and chemical environmental variables. Overall, we observed that greater dissolved oxygen concentration and shallower depths were associated with the highest fish biodiversity across lakes. Moreover, spatial comparisons additionally highlighted the importance of substrate heterogeneity and lake area as influential in determining native fish community structure. Notably, in all lakes, tilapia were relatively uncommon, comprising less than 3% of all fish captured, and their presence was not a significant predictor of indigenous fish biodiversity. Based on these results, we suggest that tilapia may have strong limitations on their population size, plausibly due to the presence of predatory native fish species, or scarce suitable ecological resources (food, breeding habitat). Conservation-focussed lake-wide management of native species via protection of core habitat characteristics may be key to promoting environmental resistance against negative effects of tilapia regional expansions. [ABSTRACT FROM AUTHOR]