In an investigation of diseases from plant-parasitizing nematodes in Henan Province, a cyst nematode was found on tobacco roots and in rhizosphere soil. We identified this strain as a new cyst nematode subspecies, Heterodera glycines sbsp.n. tabacum. The cysts and second-stage juveniles (J2) parasitizing Henan tobacco were larger than those of Heterodera glycines. A single 345-bp fragment was amplified from H. glycines sbsp.n. tabacum, whereas the 345-bp and 181-bp fragments were amplified from the soybean cyst nematode. Thus, H. glycines sbsp.n. tabacum was different from that of H. glycines. There were base transversions at 504 sites and base transitions at 560, 858, 920 and 921 sites in the rDNA-ITS sequences of H. glycines sbsp.n. tabacum compared with H. glycines, and there were base transitions at 41, 275, 278, and 380 sites in the mtDNA-COI sequences. In the phylogenetic tree based on the rDNA-ITS and mtDNA-COI regions, H. glycines sbsp.n. tabacum plants were clustered on a single branch. Based on the RAPD technique, SCAR-PCR primers were designed. A single 1113-bp fragment was amplified by specific primers (HtF1/HtR1) from H. glycines sbsp.n. tabacum, while no fragments were obtained from H. glycines. The Heterodera glycines sbsp.n. tabacum can infect soybean plants but cannot complete its life cycle. Eleven tested tobacco cultivars were infected, with an average Rf of 9.74 and a maximum of 64.2 in K326. The cumulative egg hatching rate of H. glycines sbsp.n. tabacum plants in the presence of tobacco root exudates was 42.6% at 32 days posthatching, which was significantly greater than that in the presence of soybean root exudates (30.3%) and sterile water (33.1%). In summary, the cyst nematode population parasitizing Henan tobacco was identified as a new subspecies, H. glycines sbsp.n. tabacum.