Grafted tomato plants grown in a soilless culture system in heated greenhouses in Sicily were affected by stem rot disease. Symptoms consisted of dark brown longitudinal discoloration of the basal part of the stem and petioles. Longitudinal sections of the stem revealed brown water-soaked or soft-rotted pith tissue and internal vascular discoloration. Bacterial isolates with two different colony morphologies were obtained from symptomatic tissues. Isolates were identified as Pectobacterium spp. on the basis of biochemical and molecular analyses. The analysis of the 16SrRNA gene sequence and of the concatenated sequences of the housekeeping genes rpoS and pgi revealed that the isolates of the two morphotypes belong to P. carotovorum subsp. carotovorum and P. c. subsp. brasiliensis, respectively. Isolates from both taxa reproduced disease symptoms on artificially inoculated tomato plants. This is the first report of P. carotovorum subsp. brasiliensis in Italy.