Phylosymbiosis, the association between the phylogenetic relatedness of hosts and the composition of their microbial communities, is a widespread phenomenon in diverse animal taxa. However, the generality of the existence of such a pattern has been questioned, and there seems evidence against its occurrence in small-sized aquatic animals, for which the microbiota composition is mostly shaped by local environmental factors. This study aims to investigate the microbial communities associated with poorly known marine interstitial nemerteans to uncover their microbiota diversity and assess the occurrence of phylosymbiosis. Through a comprehensive approach, specimens from various Central American sites were analyzed using morphology-based taxonomy and molecular techniques targeting the host 18S rRNA gene whereas their microbial association was analyzed by targeting the prokaryotic 16S rRNA gene. Phylogenetic and statistical analyses were conducted to examine the potential effects of host nemertean taxa and sampling locations on the host-associated microbial communities. The results provide compelling evidence of phylosymbiosis in meiofaunal nemerteans, emphasizing the significant impact of host genetic relatedness on microbiome diversity also in small-sized animals. Additional research is needed to fully unravel potential symbiotic relationships as well as the complex mechanisms that govern the relationships between hosts and their microbiota across various organisms and ecological settings. The remarkable diversity of meiofaunal animals, spanning various animal phyla with different lifestyles and inhabiting diverse ecosystems, combined with the advancements in multi-omics approaches, offers a promising avenue for comprehensive understanding of the evolutionary and ecological interactions between hosts and their microbiota throughout the animal tree of life.