In 2012, Hibiscus rosa-sinensis exhibiting enations and swelling of the veins on the undersides of the leaves were observed in San Pedro and Davao cities (Philippines). A begomovirus isolate named G2 was cloned from symptomatic leaves collected from San Pedro. The genome sequence of G2 was determined to be 2,738 nucleotides, having typical features of monopartite begomoviruses DNA-A with AV1 and AV2 open reading frames (ORFs) in the virus sense strand, AC1, AC2, AC3, AC4 and AC5 ORFs in the complementary sense strand. The genome shared 99.3% sequence identity with cotton leaf curl Multan virus (CLCuMuV) isolates GD01 (KP762786) and JS-Hi-A-3-2 (JX914662). A betasatellite molecule was associated with G2. The complete sequence of the betasatellite was 1,353 nucleotides, and shared 98% sequence identity with that of cotton leaf curl Multan betasatellite (CLCuMuB) isolate Mm (KF766950). Phylogenetic analysis indicated that both G2 and its associated betasatellite were most related with the isolates of CLCuMuV and CLCuMuB from China. This is the first report of the identification and molecular characterization of CLCuMuV infecting H. rosa-sinensis in the Philippines.