Rabbit hemorrhagic disease (RHD) outbreaks have occurred in Egyptian rabbit flocks resulting insignificant mortalities and severe economic losses. During 2021–2022, 20 samples were collected from different rabbit flocks with age range of 20 days to 6 months with high mortality rates, clinical symptoms, and post-mortem lesions attributed to rabbit hemorrhagic disease. The examined rabbit flocks were located in Lower Egypt governorates including Qalubia, Sharkia, Kafr ElSheikh, Dakhlia, Gharbia, and Behira, and in Upper Egypt governorates including Giza, Menia, Assuit, and Sohag. The present investigation aimed at molecular identification of the current rabbit hemorrhagic disease virus (RHDV) strains detected in distinct rabbit populations in various Egyptian governorates. Hemagglutination (HA) test and molecular characterization using a one-step reverse transcriptase-polymerase chain reaction (RT-PCR) targeting the partial VP60 of RHDV were utilized for identifying these agents. Sequencing and phylogenetic analysis were successfully conducted for genotyping RHDV strains. 17/20 (about 85%) farms were RHDV-positive, which was confirmed using HA test and RT-PCR. Two genotypes were identified through partial sequencing of theVP60 gene, six strains were clustered to RHDV2/b, and the other three strains were clustered to the RHDVa strain. According to the current study, RHDV2 has become the predominant strain threatening the rabbit populations in Lower Egypt governorates. On the contrary, the RHDVa strain continues to be a hazard to the rabbit flocks in Upper Egypt governorates including Giza, Menia, and Assuit.