Despite the importance of soybean in Nigeria, yields on farmers’ field have remained relatively low. The crop holds considerable potential for arresting soil fertility decline and enhancing household food nutrition. Therefore, the study was aimed at exploiting soybean genotypes differences, assessing genotype by environment effect on seed yield and rhizobia inoculation. The study was carried out in three agroecological zone of Nigeria at Abuja (Sourthern Guinea Savanna), Igabi (Northern Guinea Savanna) and Gwarzo (Sudan Savanna) during the 2015 and 2016 rainy seasons. Treatments were twenty-four soybean genotypes and three levels of rhizobia inoculation (uninoculated, inoculated with LegumeFix and NoduMax) arranged in a split plot design and replicated three times. Data were collected on percentage emergence, plant height, number of leaves per plant, chlorophyll content, number of days to 50 % flowering, number of branches per plant, number of pods per plant, total biomass yield, above ground biomass, seed yield, harvest index and 100-seed weight. Results indicated that, the variation of genotypes and inoculation on percentage emergence, height, number of leaves, number of branches per plant, total biomass yield, above ground biomass and seed yield were significant (P=0.05). In Abuja, TGx 1990- 110FN recorded the highest seed yield of 2717.5 kg ha-1 during the 2015 cropping season and TGx 1990-46F gave the highest yield of 2145.9 ka ha-1 during the 2016 cropping season. Combined data analysis revealed that TGx 1990-110FN and TGx 1989-45F gave higher seed yield of 2278.3 kg ha-1 and 1905 kg ha-1 respectively. Also, LegumeFix inoculated plants gave the highest yield of 1988.1 kg ha-1 and 2008.3 kg ha-1 for 2015 and 2016 cropping seasons. In Igabi, TGx 1989-45F and TGx 1990-110FN plants gave higher seed yield of 2154.5 kg ha-1 and 2073.6 kg ha-1 in 2015 cropping season, the same genotypes produced 2242.5 kg ha-1 and 1961.6 kg ha-1 in 2016 cropping season. Combined data showed that both genotypes gave 2198.5 kg ha-1 and 2017.6 kg ha-1 respectively. Also, LegumeFix inoculated plants produced the highest yield of 2174.5 kg ha-1 and 2262.5 kg ha-1in the 2015, 2016 cropping seasons. In Gwarzo, the seed yield among genotypes were similar for both 2015, 2016 cropping season and the combined data. Uninoculated plants produced significantly lower seed yield compared to plants treated with either NoduMax or LegumeFix. The effects of genotypes (G), environment (E) and G × E interactions on seed yield were also significant. Two soybean genotypes (TGx 1989-45F and TGx 1990-110FN) were identified as the most promising in relation to yield stability. Of the three locations, Abuja produced the least interaction effects followed by Igabi and may be most appropriate environments for large scale soybean production. Gwarzo may be appropriate for soybean evaluation as effective selection will be obtained due to relatively uniform performance of the genotypes. It is also necessary to inoculate soybean with Bradyrhizobium japonicum inoculants (LegumeFix or NoduMax) in order to enhance productivity in farmer’s field.