This study was conducted from March 2018 to January 2019 with the aim of assessing the reproductive performance and traits preferences of sheep and goats producers in pastoral and agro-pastoral area of Afar, Ethiopia. Semi-structured questionnaires and field observations were used to collect the required information from 136 from pastoral and 56 from agro-pastoral. Sheep and goats were kept for a variety of reasons including income generation, insurance (sale for cash to meet unexpected expenditures) and economic security (sale for cash to support foreseeable expenses), social/religious functions and prestige in ownership. In both production systems, next to camels, goats and sheep were ranked as the second and third most important livestock species in accordance to their relative importance. In the current study, there was a significance differences (P<0.05) in the reproductive performance of both sheep and goats between pastoral and agro-pastoral areas. Goats in agro-pastoral areas had noticeably higher average age at first kidding (12.33 ± 0.76 months), and kidding interval (8.76 ± 2.04 months) whereas they had lower age at first mating both for Doe and bucks (9.28 ± 1.85 and 7.98 ± 2.08 months, respectively). Similarly, sheep in the agro-pastoral areas had higher age at first lambing (12.30 ± 1.18 months) and lambing interval (9.16 ± 2.66 months) than sheep found in the pastoral areas. In both production systems twinning ability (0.46), fast growth (0.41) and trekking long distances were the main preferred sheep traits, whereas fast growth, milk yield and twining ability were the main goat preferred traits with an overall index value of 0.37, 0.32, and 0.32, respectively. Genetic improvement programs targeting pastoral and agro-pastoral production system need to be incorporated the traits of preference, multipurpose roles and the existing traditional herding and breeding practices.