This study assessed the breeding practice and selection criteria of dairy cows in two districts. A total number of 288 structured questionnaires were utilized to gather information from households in the study areas. Logit model, indices, and descriptive statistics were employed for data analysis. Education, marital status, and family size of respondents from Chora district were confirmed as predictors for practicing the controlled mating system and significantly influenced at p < 0.05 . The odds of practicing the controlled mating system by educated and married farmers in Chora district were 10.01 and 4.82 times higher compared to uneducated and unmarried farmers, respectively, and also, for every additional increase in family size, they increased by the factor of 1.21. Educational and marital status of farmers in Gechi district also influenced the use of controlled mating. The odds of performing controlled mating based on the educational level and marital status of the farmers were higher among educated and married individuals. Based on indigenous knowledge, teat size, udder size, and pelvic width were the 1st three ranked traits used as major selection criteria of dairy cows in Gechi district, whereas body length was the 1st among others in Chora district. This finding indicated that the combination of indigenous knowledge with modern science is important to improve cow’s genetics. The study suggests that mating systems and selection criteria should be considered as baseline information for designing the genetic improvement programs.