Symbiotic relationships between microbes and animals are incredibly common. However, most studies focus on the bacterial symbionts of vertebrate hosts and ignore both eukaryotic symbionts and invertebrate hosts. Some of the technical limitations complicating research into eukaryotic symbionts have largely been overcome, but there is an added wrinkle when examining such microbes in microscopic invertebrates. Namely, it can be difficult to distinguish eukaryotes that have simply been eaten by these tiny animals from true symbionts. To overcome this, researchers recently used phylogenetic reconstruction to identify microbial taxa that fall within typically host-associated clades. and applied this to the potential eukaryotic microbiomes of 220 marine invertebrate specimens, spanning 9 phyla. They identified numerous previously undescribed lineages and expanded the known host range of several microbial taxa. A lack of reference sequences resulted in several cryptic clades within Apicomplexa and Ciliophora, which suggests that these invertebrates harbor uncharacterized symbionts. This study represents just a tiny peek into the world of invertebrates and their potential symbionts. Yet, it still suggests that, despite their size, microscopic invertebrates harbor protist and fungal symbionts and that further research is warranted to develop more robust inferences.