Red onion has high nutrient and economic value. Onion can grow in both dry and wet season. Currently, we face climate drawbacks such as long rainy seasons and a short dry season due to climate change. This research aims to study the affects of rhizobacteria on the three red onion yield varieties. The research was conducted in Balecatur, Gamping, Sleman, Yogyakarta, Indonesia. The research used a Split Plot Design. The main factor was red onion variety, namely Bima, Biru and Thailand. The sub-factor was Rhizobacteria with a concentration of 0%, 0.75% and 1.5%. The data were analyzed using variance analysis with 5% significance level. The results showed that rhizobacteria increases the growth rate and tolerance index in red onion. Rhizobacteria does not increase yield and red onion yield index. Biru variety was as good as Thailand variety in terms of the number of bulb per plant, weight bulb per plant and yield. Thailand and Biru varieties are suitable in rainy season. Bima variety has the lowest number of bulb per plant, weight bulb per plant, growth rate, yield and yield index.