Peste des petits ruminants (PPR) is a contagious viral disease causing massive economic loss to animal industries in endemic countries including Egypt. Although a vaccine is available, coinfections can overwhelm the animal immune system and interfere with vaccine protection. Small ruminant retrovirus (SRR), including enzootic nasal tumor virus (ENTV) and Jaagsiekte sheep retrovirus (JSRV), is responsible for coinfections with PPR. Investigation of clinical cases in this study confirmed the presence of PPR virus by RT-PCR among four flocks. Sequence of five PPR amplicons revealed that all strains had 100% aa similarity and belonged to lineage IV. In addition, these strains had 98-99% nt similarity with all previous Egyptian and African strains from Sudan (MK371449) and Ethiopia (MK371449). Illumina sequencing of a representative sample showed a genome of 5753 nt compatible with ENT-2 virus with 98.42% similarity with the Chinese strain (MN564750.1). Four ORFs representing gag, pro, pol, and env genes were identified and annotated. Pro gene was highly stable while gag, pol, and env showed eight, two, and three aa differences with the reference strains. Sanger sequencing revealed that two amplicons were ENT-2 virus, and one was JSRV. ENT-2 sequences had 100% similarity with KU258870 and KU258871 reference strains while JSRV was 100% similar to the EF68031 reference strain. The phylogenetic tree showed a close relationship between the ENT of goats and the JSRV of sheep. This study highlights the complexity of PPR molecular epidemiology, with SRR that was not molecularly characterized previously in Egypt.