The current study is the first reported molecular characterization of rabbit coronavirus strains in Egypt. The cecal contents taken from young New Zealand rabbits (5-6 weeks old) with enteritis were tested for the presence of coronaviruses using RT–PCR with primers specific for the polymerase gene. The three positive samples showed the presence of the hemagglutinin-esterase (HE) gene indicative of Betacoronavirus subgroup A. Betacoronavirus strains designated as rabbit coronavirus (RCoV) Egypt/Qal/1, RCoV Egypt/Qal/2 and RCoV Egypt/Qal/3 were partially sequenced for their HE and spike (S) genes. In all RCoV Egypt/Qal strains, the nucleotide homology was 98.3-100% and 99.8-100% for HE and S genes respectively while the deduced amino acid homology was 98.7-100% and 99.5-100% for HE and S proteins respectively with characteristic cleavage site QGRSRR motif in their S proteins. High similarity was observed with RCoV HKU14 strains and bovine coronavirus strains (BCoV) than other Betacoronaviruses. Phylogenetic data of nucleotide and amino acid sequences of the HE and S genes revealed that all RCoV Egypt/Qal strains were more homologous to each other and were distinct from the other known Betacoronavirus published on GenBank. The findings suggest the existence of a novel variant of RCoV genetically related to RCoV HKU14 strains