In April 2001, reduced leaf size, leaf curling, yellowing symptoms, and reduced yield were observed in tomato plants in the southwestern (Toliary, Morondava, Miandrivazo) and northern (Antsiranana) regions of Madagascar. Symptoms were similar to these caused by Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae). Large populations of Semisia tabaci (Gennadius) were observed colonizing tomato, other crops, and weeds. Leaf samples were collected from tomato plants from 14 sites located in northern, central, and southern Madagascar. Two plant samples collected near Antsiranana, one sample near Morondava, and one sample near Toliary were positive in triple-antibody sandwich enzyme-linked immunosorbent assay using a begomovirus-specific antibody purchased from ADGEN (Nellies Gates, Auchincruive, Scotland, UK). A 500-bp product was amplified and cloned (2) from two leaf samples collected near Toliary and one near Morondava using a pair of degenerate primers that are expected to amplify a region of the A component of begomoviruses between the intergenic conserved nonanucleotide sequence and the first 200 nucleotides of the coat protein ORF. The sequences corresponding to (he two Toliary samples (GenBank Accession Nos. AJ422123 and AJ422124) and the Morondava sample (GenBank No. AJ422125) showed the most significant alignments (NCBI, BLAST) with begomoviruses, Tobacco leaf curl virus from Zimbabwe (GenBank Accession No. AF 350330) and Tomato leaf curl virus from Tanzania (GenBank Accession No. U73498) with 76 to 77% nucleotide identity (Clustal method, MegAlign, DNASTAR, London) and South African cassava mosaic viruses (SACMV GenBank Accession Nos. AJ422132 and AF155806) and East African cassava mosaic viruses from Malawi (GenBank Accession Nos. AJ006459 and AJ006460) with 74 to 75.5% nucleotide identity. The low nucleotide identity suggests that the begomovirus isolated from tomato in Madagascar is a new species. Since the core region of the coat