Host associated bacteria face a different set of dispersal challenges since they often depend on their hosts providing specific environments compared to the surrounding. Here we investigate the impact of biogeographic distances on the bacterial diversity and composition of Ampullaceana balthica-gastrointestinal tract bacteria. Effects on the host-associated bacterial community are compared to water and sediment communities using 16S rRNA gene sequencing. The bacterial communities sampled in Estonia, Denmark and Northern Germany differed between water, sediment and gastrointestinal tract and also between countries within each substrate indicating that each substrate has specific communities. The turnover rate over increasing geographic distances were lowest for gastrointestinal tract and highest for water bacterial communities. Also, the overlap of 16S rRNA gene amplicon sequencing variants (ASVs) between countries was lowest for gastrointestinal tract bacteria. The low turnover rate of the gastrointestinal community combined with little ASV overlap between counties suggests unspecific ASVs colonization from the local bacterial communities. It also supports that the host applies little phylogenetic selection on its gastrointestinal bacteria. The resulting country specific gastrointestinal bacterial community that is independent from the geographic distance supports that the gastrointestinal tract can act as habitat islands despite being strongly influenced by local environmental factors.