This study characterized indigenous chicken (IC) ecotypes morphologically. Five IC ecotypes studied were Kakamega (KK), Siaya (BN), West Pokot (WP), Narok (NR) and Bomet (BM). Data on morphological features were collected from 1 580 chickens and 151 for zoometric measurements. Descriptive statistics, non-parametric and F tests were used in analysis. A non-parametric Kruskal–Wallis, Binomial test and Mann–Whitney U test was used to evaluate whether the ecotype have effects on the qualitative morphological variables. Zoometric measurements was analysed with the PROC GLM of SAS. Results revealed that, black, black-white striped, brown and red body plumage colours were significantly different (P <0.05) between the ecotypes. Feather morphology (%) were not significantly different (P > 0.05). Distribution of body feathers (%), comb types (%) and zoometric measurements were significantly different (P <0.05). Eye colours varied significantly (P <0.001) within the ecotypes unlike between the populations. In conclusion, IC ecotypes studied are heterogeneous population with huge variability in morphological features.