This study was designed to characterize N gene sequences of Peste des Petits Ruminants Virus (PPRV) isolates circulating in Pakistan and to evaluate the efficacy of available diagnostic assays on local isolates. During the study period, a total of sixty PPR outbreaks were investigated. A total of 20 selected samples from these outbreaks were sequenced for N gene. The results analysis and the phylogenetic trees indicated two different viral groups in N gene; one was closer to China and Tajikistan while other group was similar to isolates from Iran and Saudi Arabia. Efficacy of three commercially available tests for the antigen detection of PPR, i.e., Peste test, Enzyme linked immuno-sorbent assay (ELISA) and Reverse transcriptase polymerase chain reaction (RT-PCR) was compared. Keeping PCR as gold standard, sensitivity was calculated as 85% and 57% and specificity was calculated as 83% and 79% for ELISA and Peste test, respectively. Value of K for ELISA was 0.67 which indicates good agreement between ELISA and RT-PCR. Value of K for Peste test was 0.33 which indicates fair agreement between Peste test and RT-PCR. In conclusion, study provides premier information about the use of different diagnostic tests and molecular situation of PPRV in Pakistan.