Tomato (Solanum Iycopersicum) belongs to the family Solanaceae. All species are diploid (2n= 24). India ranks third in area and production worldwide with an area of 0.69 million ha and production of 11.97 million tons. It is the second most important vegetable crop in Meghalaya. The cultivated species is susceptible to diseases like early blight, late blight and Fusarium wilt, etc. and insect pest infestation from mites and aphids. Thus,gene transfer becomes necessary. However, problems of crossability have resulted in limited success in gene transfer programmes. The present study was carried out to determine if the problem of crossability is due to pre- fertilization or post- fertilization barriers, and to standardize the optimum stage and medium for embryo rescue of the immature embryo and to confirm the hybridity of the rescued plants using molecular markers. The species Solanum Iycopersicum (MT-3) had maximum number of viable pollen (94%) whereas the species Solanum peruvianum (WIR-3957) had the least number (55%). Variability of pollen germination was observed in selfing, inter-specific and reciprocal crosses. The pollen from the various crosses start germinating 8 hours after pollination and the number of germinating pollen increased further. S. Iycopersicum (MT-3) also recorded maximum pollen germination (44%) and pollen tube growth (623 \-1m).The pollen germination at 24 hours after pollination showed a positive correlation with fruit set. The cross of S. Iycopersicum with S. pimpinellifolium gave the maximum fruit set followed by the reciprocal cross while there was not much difference in the pollen tube growth after 24 hours. S. Iycopersicum x S. peruvianum showed only 7-8% fruit set and the pollen tube growth was also less.Maximum fruit set was recorded in the selfing of S. Iycopersicum (MT-3) andlowest fruit set was recorded in the interspecific cross of S. peruvianum as female parent with S. Iycopersicum (MT-3) and S. Iycopersicum (KA). S. Iycopersicum (MT-3) also recorded maximum pollen germination and pollen tube growth. Twenty five days after pollination was found to be the optimum stage for rescuing the immature embryos. MSmedium supplemented with 1 mg/I GA3, 0.1 mg/I NAA and 0.5 mg/I BAP gave the highest germination percentage of the cultured embryos. Hybridity of the embryo rescued plants was confirmed using RAPD markers. Confirmation of hybridity was best resolved withprimer OPAB-18 which gave unique bands at 550 bp and 350 bp in both the male and rescued hybrid plants of S. Iycopersicum (MT-3) x S. peruvianum and S. Iycopersicum (KA) x S. peruvianum. The primer OPAB-17 also gave results which confirmed the hybridity of the embryo rescued plants.