The flagellate protist communities are an important part of the termite, as they lead the lignocellulose digestion. Termites (Reticulitermes grassei) were sampled from forest and urban environments in mainland Portugal where they are native and in Faial Island, Azores (invasive populations). Termites’ gut contents was analysed morphologically and the diversity of the flagellate protist community evaluated based on morphotypes. From the two Azorean invasive populations we were able to identify 12 different morphotypes whereas some of the populations in the mainland had as few as 6. Indeed, on the fourteen native populations the number of flagellate protists morphotypes ranged between 6 and 12. Shannon Wiener diversity index was used to calculate a variation partitioning between geographical and local variables. Our results suggest the existence of a core group of flagellate protists, probably performing key steps in the lignocellulose digestion. However, these communities may be more diversified and factors linked with the geographic location are likely a key influence of the flagellate protist communities analysed. In the invasive urban termite populations the high flagellate protist communities’ diversity, as well as the similarity between the two populations captured, may indicate a switch of R. grassei foraging and social habits in the invasive termite populations. Local conditions also influenced the flagellate protist communities, although not so markedly as geographic location. In this study, native termite colonies from urban environments showed the less diverse flagellate protist communities.

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