A begomovirus was recently shown to be causing Jatropha mosaic disease (JMD) on Jatropha for the first time in India. A typical begomovirus-like symptoms characterized by chlorotic specks on leaves, curling and malformation of leaves, severe reduction in leaf size, partial or complete sterility were seen on infected plants. In Karnataka state, South India, JMD caused significant yield losses by affecting the growth of the infected plant and by disease incidences of up to 47%. The putative Jatropha mosaic India virus (JMIV) was successfully transmitted through grafting, the dodder Cuscuta subinclusa and the whitefly, Bemisia tabaci. The JMIV was detected in infected plants and individual B. tabaci by polymerase chain reaction tests using two sets of begomovirus-specific degenerate primers. The core coat protein (CP) sequences of ~575 bases were obtained from two isolates collected at Bangalore and Dharwad, South India. Phylogenetic analysis of the core CP sequences with those of selected begomoviruses grouped JMIV in a separate cluster close to Indian cassava mosaic virus and Sri Lankan cassava mosaic virus and shared highest nucleotide identities (90-95%) with them. The two JMIV isolates were 94% similar to each other. The begomoviruses causing JMD in the Americas grouped separately from JMIV and shared only 72.8-75.2% core CP nucleotide identities thus they are distinct. These results further confirm that JMD in India was caused by begomoviruses and they were most closely related to cassava mosaic viruses from the Indian sub-continent.