This paper presents a new phylogenetic estimate of isopod crustaceans of the suborder Asellota with the aim of clarifying the evolution of the superfamily Janiroidea, a large and diverse group inhabiting all aqueous habitats. The phylogenetic analysis is based on a morphological evaluation of characters used in past classifications, as well as several new characters. The evolutionary polarity of the characters was determined by outgroup analysis. The characters employed were from the pleopods, the copulatory organs, the first walking legs, and the cephalon. The resulting character data set was analyzed with numerical phylogenetic computer programs to find one most parsimonious clado-gram, which is translated into a classification using the sequencing convention. The new phylogenetic estimate is significantly more parsimonious than previous trees from the literature, and several of its monophyletic groups have robust confidence limits. The superfamily Stenetrioidea belongs to the clade including the Janiroidea, not with the Aselloidea as previously suggested. The sister group of the Janiroidea is the family Pseudojaniridae, which is elevated to superfamily rank. The clade including the families Gnathostenetroididae and Protojaniridae is not the sister group of the Janiroidea, and is derived earlier in janiroidean evolution than the Stenetrioidea. Within the Janiroidea, the family Janiridae is not the most primitive taxon as previously believed. The clade including the families Munnidae and Pleurocopidae contains the earliest derived janiroideans. The data also indicate that the unusual sexual morphology of the Janiroidea did not appear suddenly but developed as a series of independent steps within the Asellota.