Begomovirus was identified as one of the causal agents causing yellow mosaic disease on yard long bean (Vigna unguiculata subsp. sesquipedalis L.) in Java. Research was conducted to characterize the virus based on its nucleotide sequences. Research was started by field survey to collect leaf samples, followed by virus detection using polymerase chain reaction and analysis of virus sequences. Samples from Tegal, Klaten, Magelang, Cirebon, Subang, and Bogor were positively infected by Begomovirus based on specific viral DNA amplification. Sequence analysis indicated that Begomovirus infecting yard long bean belongs to the same group with Mungbean yellow mosaic India virus (MYMIV) from Bangladesh, India, Pakistan, and Nepal. Further analysis showed the conserved region of Begomovirus around Common Region, i.e. “TATA box” Sequence, Hair Pin Loop Structure, Repetitive Sequence, and the Conserved Nonanucleotide Sequence TAATATTAC.