Goat population is increasing at a faster rate (4%) than other co-existing livestock species in Pakistan. Four indigenous goat breeds of Khyber Pakhtunkhwa, Pakistan i.e. Gaddi, Damani, Kaghani and Surgoli were sampled from their home tracts for morphological and molecular characterization. A total of 120 samples (30 of each breed) were studied. Gaddi was of largest size manifested by large body length, chest girth, ear blade width, head length, heights and horn length and was the heaviest in weight compared to other breeds. Both Kaghani and Gaddi breeds have long and glossy hair with coat color of white, black or grey. Surgoli and Damani have medium hair, white, red, black or brown in colour. Most Kaghani and Gaddi have beards, less common in Surgoli and Damani. No wattle was observed in Kaghani or Gaddi breeds but present in Damani and Surgoli. All the four breeds have horns and no polled individual was seen. Morphologically Damani has screwed 56.7% and Gaddi have curved horns 66.7% while Kaghani and Damani have 83.3% and 43.3% spiral horns respectively. Gaddi and Kaghani showed better performance as compared to Damani and Surgoli especially in terms of milk and meat production. Total of 30 SSR markers were used of which 24 were amplified. In total 130 alleles were detected. Surgoli was the most diverse breed and the least was Gaddi. Mean number of alleles, effective number of alleles and unique alleles were 5.42, 3.89 and 11 respectively. Average genetic diversity was 0.689, the highest in Surgoli i.e. 0.7228.F indics (FIT), (FST) and FIS were calculated as 0.706, 0.075 and 0.670 respectively. All pair wise estimate of population differentiation was significant P<0.05. Mean Nm (gene flow) value was 2.92 migrants per generation. Average observed and expected heterozygosity was 0.219 and 0.727 respectively. PIC of 0.585 showed that most markers are highly polymorphic. Allelic richness ranged from 4.00 to 4.71. The Bottle neck analysis showed that Gaddi, Damani and Surgoli were in a state of mutation drift equilibrium while Kaghani deviated from mutation drift equilibrium. This instability of the population is an evidence of genetic bottleneck. Phenotypic and molecular characterization of animals is much needed for conservation and designing improvement strategy for these genetic resources of a country.