This study aimed at determining chicken genotypes of choice and traits preference in chicken by smallholder farmers in Nigeria. Data were obtained from a total of 2063 farmers using structured questionnaires in five agro-ecological zones in Nigeria. Chi square (χ²) statistics was used to explore relationships between categorical variables. The mean ranks of the six genotypes and twelve traits of preference were compared using the non-parametric Kruskal–Wallis H (with Mann–Whitney U test for post hoc separation of mean ranks), Friedman, and Wilcoxon signed-rank (with Bonferroni’s adjustments) tests. Categorical principal component analysis (CATPCA) was used to assign farmers into groups. Gender distribution of farmers was found to be statistically significant (χ²?=?16.599; P?≤?0.002) across the zones. With the exception of Shika Brown, preferences for chicken genotypes were significantly (P?≤?0.01) influenced by agro-ecological zone. However, gender differentiated response was only significant (P?≤?0.01) in Sasso chicken with more preference by male farmers. Overall, FUNAAB Alpha, Sasso, and Noiler chicken were ranked 1st, followed by Kuroiler (4th), Shika Brown (5th), and Fulani birds (6th), respectively. Within genotypes, within and across zones and gender, preferences for traits varied significantly (P?≤?0.005 and P?≤?0.01). Traits of preference for selection of chicken breeding stock tended towards body size, egg number, egg size, and meat taste. Spearman’s rank order correlation coefficients of traits of preference were significant (P?≤?0.01) and ranged from 0.22 to 0.90. The two PCs extracted, which explained 65.3% of the variability in the dataset, were able to assign the farmers into two groups based on preference for body size of cock and hen and the other ten traits combined. The present findings may guide the choice of appropriate chicken genotypes while the traits of economic importance may be incorporated into future genetic improvement and conservation programs in Nigeria.