Cucurbit crop production was seriously damaged by begomovirus diseases in Southeast Asia. However, the related information on this virus is shortage in Malaysia. In 2016 and 2017, the viral diseases in cucurbit production fields were observed in Eastern and Western Malaysia, and the disease incidence up to100% with symptoms of mosaic and yellow leaf curling was investigated. Seventy symptomatic samples were collected in 7 cucurbit crops from 15 locations, and 51 symptomatic cucurbit samples were tested for presence of begomovirus by PCR using primer pair- PAL1v1978B/PAR1c715H. Fifty-two PCR products were sequenced from selected 45 samples. Based on the phylogenetic analysis, those 52 sequences were grouped into five clusters. Considering the demarcation criteria 91% nucleotide sequence identity for virus species and 94% for virus strain, the majority Tomato leaf curl New Delhi virus (ToLCNDV) isolates were distributed in four clusters and could be considered respectively belonging to distinct strains. The Squash leaf curl China virus (SLCCNV) isolates from Eastern Malaysia formed the other cluster. Both SLCCNV and ToLCNDV are first detected in Malaysia, and the whole viral genomic DNA sequencing is ongoing for further characterization. However, our results reveal the explanting of cucurbit-infecting begomoviruses in Southeast Asia, and should be considered seriously as an important factor for cucurbit virus control in the area.