Although the role of gender play a great role in the livelihoods of greater portion of rural households in the study area, the participations level on the activities of the agricultural production is little focused. This study, therefore was designed to assess gender participation and integration constraints in Gedeo and Alaba Zones in southern Ethiopia. The study was designed in cross sectional design. The data were collected in two zones, 3 woredas, and 8 rural kebeles. Samples who randomly selected were 86 men and 69 women farmers a total 155 farmers were selected so as to collect the required data through triangulation of different tools, which are key informants interview, focus group discussion and household survey and the data was analyzed using descriptive statistics, participation index scoring and ordered logit analysis. Based on the data analysis result frequency of men and women participation in selected agricultural practices were computed. There were six gender participation factors evaluated in descriptive statistical tools, based on the respondents, 118(76.2%) respondents believed that community norm can affect the participation of gender in agricultural practice and 1(0.6%) respondent believed that cultural norms couldn’t affected by community norm. The average task share of the household is 30%, 15%, 43% and 12% for men, boy, women and girl, respectively. Women and men performed larger share of the gender role in rural household as compared to boys and girls. The reproductive work of women in the household covered 67% of the total household care work. Generally the gender participation index was 73.8 which indicated that the gender participate on all agricultural activities but concerning to women it needs effort to amend the factors affecting women participation. Even though the gender role of boys and girls in selected agricultural commodities is very low, they were highly engaged in their academic persuasions in school and at home. According this statistical result household members spent agricultural labor hour in differently, as converted this labor share in to daily labor hours indicated that women, men, boys, and girls are spending 10, 7, 4 and 3 hours per day on average, respectively. Results obtained from the ordered logit model indicated that institutions, awareness level, opportunities to agricultural extension, credit access, education level and land size showed positive significant relationship with their gender participation in farming activities Women are just as efficient agricultural producers as men and can achieve similar yields when given access to resources, including training and services. Therefore, increasing the opportunities for women and youths can have a powerful impact on productivity and agricultural-led growth and are recommended for better rural development.