As selective breeding programs are time-consuming and expensive, it is critical that clients preferred traits are accurately identified. This is important to achieve value for money and adoption of selectively improved fish, and an essential foundation for effective contributions of genetic improvements to farming system. Data on fish trait preferences of smallholder farmers are rare; when these do exist, there is no information on whether the preferences of men and women are similar or not. The present work reports the first gender-disaggregated study of trait preferences of men and women from farming households for rohu carp (L. rohita) in Bangladesh (288 respondents) and India (270 respondents), addressing a major segment of aquaculture production in south Asia. The paper generates a nuanced, novel, and comparative understanding of the preferred characteristics through a survey of smallholder farmers that: 1) uses open-ended questions relating to producer and consumer perspectives; and, 2) applies a stated choice experiment using 1000minds software to address trade-offs in choices between traits for a subset of (58–38) respondents. General preferences derived from expressed likes or dislikes emphasized the importance of good taste, characteristics indicating freshness and safety such as aspects of appearance and color, as expected for a perishable product, and of value for money, including size of fish or relative flesh quantity. The overall pattern of preferences were similar for men and women, but there were differences in that men focused more on economic-related characteristics and women more on characteristics associated with nutritional value and food safety. When producers identified what to improve, they focused on larger size fish, reduced culture period, fry survival and disease resistance. When choosing between traits in pair-wise comparison exercises, ranking of traits was similar for both men and women in both Bangladesh and India. Significant differences were only observed between genders for the lower ranked traits in Bangladesh. Larger size fish as a charateristic ranked first in all groups, but there were marked differences between the importance of price and taste in the two countries. Methodologically, the study demonstrated that general preferences, do not automatically translate into characteristics for improvement by breeding programs, and the latter were not necessarily an accurate guide to the preferences expressed when specific tradeoffs were considered. These findings emphasize the need for well-designed and targeted surveys to be able to accurately define trait preferences, in particular to identify the relative values of heritable traits for practical application in breeding programs.