Avian orthoreovirus (ARV) imposes substantial economic losses on the global poultry industry, primarily through runting–stunting syndrome and viral arthritis. Despite its global prevalence, the molecular epidemiology and pathogenic landscape of ARV strains circulating in Upper Egypt remain largely unexplored. This study investigated the molecular characteristics, phylogenetic relationships, and pathogenic potential of ARV in broiler flocks across Assiut, Sohag, and New Valley governorates. Out of 140 clinical samples from chickens showing stunted growth and tendon swelling, 42 (30%) were positive by RT-qPCR targeting the σC gene. Phylogenetic analysis of 11 representative isolates using MEGA X revealed a complex co-circulation of two genetically distinct genotypes. Notably, this study provides the first report of ARV Genotypes IV (GC IV) and V (GC V) in Upper Egypt governorates. Nine isolates clustered