Fasciolosis is an important zoonotic disease affecting domestic animals in most parts of the world. Two important species of flukes Fasciola (F.) gigantic and Fasciola hepatica with an intermediate form was reported by many researchers from different countries of the world. For identification of species of fasciolids 167 flukes were collected from domestic animals at abattoirs from three topographic locations from three districts of Azad Jammu and Kashmir during 2012. Readings were taken using glass rulers and ocular micrometer. Characterization of F. hepatica revealed average length (mm) 20.66±2.27 to 23.20±5.25 and width 9.90±0.50 to 10.16±1.00 and that of F. gigantic 41.25±1.55 to 45.33±0.83, 9.44±0.20 to 9.71±0.37 respectively. It was noted that F. hepatica predominantly affecting animals at high altitudes with cooler climate and F. gigantica at low altitudes with warm conditions. No “intermediate form” of fasciola was found at any location or host animal. All flukes after morphometery were identified through PCR using species specific primers. Further investigations are required to investigate intermediate form from different geographic locations of Pakistan for control measures.