Morphologically similar species, that is cryptic species, were long considered as taxonomic artefacts. However, recent evidence suggests that cryptic species complexes may be similar or quasi-similar owing to the deceleration of morphological evolution, though the factors underlying deceleration remain unknown. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the phylogenetic history of the species complex. We explore population structure and use population-level statistics to determine the degree of connectivity between populations and species. We find that the combination of WGA and ddRAD allows us to obtain genomic-level data from microscopic eukaryotes (~1 millimetre) opening up opportunities for those working with population genomics in such taxa. The three species share genetic variance, likely due to incomplete lineage sorting maintaining ancestral polymorphism. We suggest that the degree of shared variation might underlie morphological similarity in the Stygocapitella cryptic species complex.