The study was conducted to characterize the variations in physical characters and some important feather and skin mutations observed in different populations of native chickens of West Bengal and Sikkim, India. The data encompassing eight different phenotypes such as, naked neck chicken, frizzled chicken, muffed/bearded chicken, creeper chicken, crested chicken, rumpless chicken, feathered shank chicken and fibromelanosis chicken, were collected from six districts of West Bengal and two districts of Sikkim. Seven qualitative traits such as colour of the egg shell, feather, skin, shank, comb and earlobe as well as the type of feather, and three quantitative traits such as shank length, egg weight and body weight, were assessed in a total of 2 170 fowls of both sexes. The data were analysed statistically using descriptive statistics, the differences in means were compared using Duncan's multiple range test and χ2 was used for non-parametric characters. Each of the populations had multiple variants and mixed feather colours were seen in most of the chickens while the feather, skin and shank colours were all black in fibromelanosis chickens. The shank colour was predominantly blue, followed by yellow and white. The skin colour in most of the chickens was white. Most of the chickens had a single comb (except for the crested chicken). The highest body weight was observed in the desi chicken while the rumpless chicken weighed the least. The egg-shell colour varied between cream and light brown in all the flocks except for the fibromelanosis chicken whose egg-shell colour was tinted bluish. The highest recorded egg weight was observed in the naked neck chicken, whereas the hatchability and egg weight were the lowest for the rumpless chicken. In the recent years, it has been observed that there is a significant reduction in the population of native chickens. This may be attributed to the restocking with Rhode Island Red and synthetic Kruilor chickens following the avian influenza outbreaks in the region. Hence, immediate steps need to be taken to preserve whatever is left in the native chicken ecotypes in the region.