Germplasm accessions of Trifolium nigrescens Viv. were found to belong to three distinct taxa which differed in morphology, hybrid seed-set in crosses among themselves and with white clover (T. repens L.), chromosomal distribution of rDNA genes, and rDNA internally transcribed spacer (ITS) region sequences. These taxonomic groups correspond with T. nigrescens ssp. nigrescens, T. nigrescens ssp. petrisavii var.petrisavii and var. meneghinianum. The existence of var. meneghinianum has been rejected or ignored in recent taxonomic treatments. The present study indicates that it is very distinctive and warrants at least subspecies status. Phylogenetic analysis based on ITS sequences and pod morphology placed ssp. nigrescens as progenitor to the others. ITS sequences placed white clover closer to ssp. petrisavii but neither DNA sequences nor rDNA chromosome locations clearly showed whether var. petrisavii or var. meneghinianum was closer to white clover. In contrast, results of hybridization studies showed that ssp. nigrescens gave full seed-set when pollinated with T. repens whereas both ssp. petrisavii var. petrisavii and ssp. petrisavii var. meneghinianum gave poor seed-set. All three taxa showed close relationships with white clover and none can clearly be shown to be a direct ancestor of T. repens.