Peste des petits ruminants virus (PPRV) is the aetiologic agent of Peste des petits ruminants (PPR), an important viral disease of sheep and goats. PPR is endemic in Nigeria and leads to social and economic losses. The objective of this study was to determine the prevalence of PPR infection and genetically characterize PPRV strains obtained from sheep and goats in three States of Southeast Nigeria. A total of 285 nasal swab samples collected in 2017‑2018 were processed for PPRV genome detection by RT‑PCR. Sixty‑five (22.81%) of the samples were positive for PPRV. Sequence and phylogenetic analyses revealed that the PPRV belonged to lineages II (11/38, 28.9%) and IV (27/38, 71.1%). The N gene fragment sequence showed a 99.77%‑100% and 99.98%‑100% identity among the strains of lineages II and IV, respectively. Fourteen amino acid substitutions, previously unreported in PPRV strains from Nigeria, were recorded. This study confirms the circulation of PPRV lineages II and IV in Southeast Nigeria, the dominance of strains belonging to lineage IV in recent years, and their close genetic relationship with those previously reported in other parts of Nigeria and neighboring countries.