The exceptional hidden diversity included in the squat lobster genus Phylladiorhynchus and its wide bathymetric and geographic range make it an interesting group to thoroughly study its evolutionary history. Here we have analyzed the entire currently known species diversity of Phylladiorhynchus using an integrative approach that includes morphological and molecular characters. The aim was to establish whether depth range (bathymetry) has played a role in their morphological and molecular evolution and in their diversification pathways. Phylogenetic analyses recovered the genus as monophyletic and as the sister group of Coralliogalathea, conforming with current systematic hypotheses, although their placement in a monophyletic Galatheidae is doubted. All the analyzed species represent well-supported lineages, structured in ten clades, correlated in most part with the morphological phylogeny. The reconstruction of ancestral habitat showed that the most recent common ancestor of Phylladiorhynchus most likely lived in shallow water environments. The divergence time estimation analyses dated the origin of the genus back to the Upper Jurassic, preceding the origin of all the other galatheoid lineages. Morphological analyses suggested that species from deeper waters exhibit greater morphological divergences and lower genetic divergences in comparison to species from shallower waters. In Phylladiorhynchus, the colonization of deeper waters has taken place independently multiple times since the Lower-Cretaceous. Our reconstruction of ancestral habitat suggests that shallow waters ancestors might show an acceleration in the molecular rate of evolution in comparison to deep sea lineages, and a slowdown in the rates of morphological evolution. However, although lineages from shallow and deep sea habitats show slight differences in diversification trends, bathymetry does not significantly affect the diversification rate in Phylladiorhynchus according to our diversification analyses.