Four different DNA extraction protocols were compared for ability to produce DNA from the various tissues (caudal fin, pectoral fin, pelvic fin, muscle and gills) of three different freshwater fish species (Hypophthalmichthys molitrix, Labeo rohita and Sperata sarwari). Study describes the comparison of Phenol-chloroform; salt extraction; TNES and Urea methods in terms of ability to extract high quality yield and amplifiable DNA from the various tissues of fish species available in Pakistan. Although notable variations were by mean of purity and yield of quality DNA were observed among study methods, all our methods produced DNA suitable for PCR amplification. The DNA obtained from all methods were quantified and tested by Polymerase Chain Reaction. Test results indicated superiority of one out of four protocols, Phenol chloroform method a least hazardous and simplest in order to perform, a significant higher DNA yields were found than other studied methods.