Peste des petits ruminants (PPR) is an endemic disease of small ruminants, and vaccination has been the method of control but outbreaks are continuously occurring in Pakistan. The following study presents a detailed investigation of an outbreak, suspected to be PPR, probably introduced by PPRV-infected sheep and goats from Sindh Province (north-west) to Punjab Province (central) of Pakistan during the flood relief campaign in 2011. A total of 70 serum samples from 28 different flocks were tested with competitive ELISA (H antibodies), which detected 24 (34.2%) samples positive for PPRV antibodies. Nasal swabs and faeces were tested with immunocapture ELISA (N antigen), which detected 18 (25.7%) samples positive for PPRV antigen. The RNA detected positive (n = 28, 40%) using real-time PCR was subjected to conventional PCR for the amplification of the fusion and nucleoprotein genes. Sequencing of both genes and subsequent phylogenetic analysis indicated the grouping of all the sequences to be in lineage IV along with other Asian isolates of PPRV. However, sequences of both genes were divided into two groups within lineage IV. One group of viruses clustered with previously characterized Pakistani isolates, whereas the other group was distinctly clustered with isolates from the Middle East or India. The sequence identity indicated the introduction of at least one population of PPRV from a different source and circulation in the local flocks of small ruminants, which emphasized the need to obtain health clearance certificate before movement of animals. The results of this study provide baseline data for the genetic characterization of different PPRV populations in Pakistan.