Three cytoplasmic male sterile (CMS) lines and their respective maintainer lines of rice were used in this experiment. The CMS lines included the newly developed line 'Pant CMS 3A' along with the two existing CMS lines, IR58025A and Pusa 6A. These were planted in four rows of 6 meter length along with two rows of the respective maintainer lines by the side. The hybrid seed set under natural out crossing conditions was allowed without the application of GA3 and supplementary pollination. Observations were recorded on plant height, tillers/plant, days to 50% flowering, panicle exertion (%), out crossing rate (%) and total hybrid seed production. Pant CMS 3A showed significant advantage over the two widely used CMS lines, IR58025A and Pusa 6A with respect to all the important traits. The panicle exertion in CMS 3A was 96.7% compared to 72.3% in IR58025A and 71.2% in Pusa 6A. Similarly the out crossing rate in CMS 3A was 31.8% compared to 8.7% in IR58025A and 16.3% in Pusa 6A; and the hybrid seed yield in CMS 3A was 1998 kg/ha compared to 1203 kg/ha for IR58025A and 1173 for Pusa 6A. These results indicate that by using the new Pant CMS 3 line, the yield of hybrid seed can be doubled and the use of GA3 can be avoided. At molecular level Pant CMS 3A was found most similar with its corresponding maintainer line, Pant CMS 3B (97%). However, the similarity values for Pusa 6A and IR58025A with their maintainers, Pusa 6B and IR58025B was recorded 93% and 87% respectively.