The study was conducted to characterize the fat-tailed and thin-tailed sheep breeds based on morphological traits and low-density SNP markers. Six hundred and five animals were used from both fat-tailed and thin-tailed sheep breeds for phenotypic observation and body linear measurements and two hundred and seventeen animals were used for molecular studies. Both qualitative and quantitative data were collected and analyzed using SAS 9.4. The measure of the genetic diversity within the breed and genetic relationships and distance between breeds were analyzed using ARLEQUIN 3.5.2 software. Genetic structure among breeds was analyzed using a model-based clustering algorithm implemented in the software ADMIXTURE v. 1.2.3 and the pattern of breed admixture was further analyzed through principal component analysis (PCA) using the GenABEL R package. Diverse coat color pattern and coat color type were observed in both fat-tailed and thin-tailed sheep breeds. Least square means and standard error of body weight and linear body measurements of fat-tailed and thin-tailed female sheep showed a significant (p