Mesophaenocora polyova is a new species discovered in temporary ponds in Uruguay. It has testicles and vitellaria in grape-like bunches, the genital atrium is V-shaped and differentiated into two regions (male and female) and the bursa copulatrix is absent. A seminal receptacle and ‘vesicula resorbiens’ are present. This combination of characters distinguishes Mesophaenocora from the other genera in the Typhloplanidae. A preliminary cladistic analysis of subfamily relationships places the new taxon in a high position in the tree. The new subfamily belongs to a clade within the subfamilies Mesostominae and Phaenocorinae, showing affinity between these three taxa. The erection of this new subfamily is supported by cladistic analysis.