Tomato production is limited by many biotic stresses of which root knot nematode (RKN, Meloidogyne incognita) is a major pest. The present study aimed to identify resistance sources in controlled conditions and compare molecular markers for efficient and rapid screening of M. incognita resistance. Among the ten genotypes evaluated, HAT-310 and HAT-311 were found immune to M. incognita infestation. Further, six crosses with these two resistant sources, (HAT-311 x Swarna Lalima, HAT-296 x HAT-311, EC-596747 x HAT-311, Swarna Lalima x HAT-310, EC-596743 x HAT-310 and Swarna Lalima x HAT-311), exhibited immune responses against M. incognita. Four molecular markers viz. JB-1, REX-1, PMi12 and Mi23 were employed in eighteen germplasm to characterise resistance and susceptibility of the genotypes against infestation by M. incognita. JB-1 yielded 420 bp in all the genotypes after digestion and hence could not be used to differentiate between nematode resistance and susceptibility. Marker PMi12 yielded additional DNA fragments in addition to the expected bands and did not give consistent results. REX-1 and Mi23 markers successfully differentiated between nematode resistant and susceptible genotypes. Moreover, Mi23 separated the homozygous and heterozygous resistance sources since the restriction enzyme analysis was not needed. The resistant genotypes identified from the present study may be used further in nematode resistance breeding programmes of tomato and the Mi23 marker can be used for rapid screening of the germplasm.