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Background: Sporadic flowering contributes significantly to genetic diversity and connectivity among populations. Woody bamboos present sporadic or gregarious flowering patterns with long flowering cycles. In this study, we analyze the genetic diversity of three Guadua species distributed along the Gulf of Mexico slope that have different patterns of flowering. Questions: (1) Are the three Guadua species genetically differentiated? (2) Does the vulnerable species G. inermis have low levels of genetic diversity? (3) What is the relative contribution of geographic and environmental factors to the genetic structure of G. inermis? Species studied: G. amplexifolia, Guadua inermis and G. tuxtlensis. Study site and dates: During 2014 and 2015, we collected samples of G. inermis in Puebla and southeastern Mexico, G. amplexifolia in Veracruz and Oaxaca, and G. tuxtlensis in southern Veracruz. Methods: We successfully amplified five of nine SSR markers, and genotyped a total of 155 samples. Results: The three Guadua species were genetically differentiated. For G. inermis, we found high levels of population genetic diversity, which are relatively higher than those of other monocot species. Genetic differentiation was high and three groups were detected: north, central and south. We found a significant association between genetic distances and the maximum temperature of the warmest month, but not with geographic distance. Conclusions: Our study is the first to analyze levels of genetic diversity in Mexican bamboos and confirms their taxonomic identity. G. inermis has a strong genetic structure, even when populations are geographically close.