Tomato yellow leaf curl disease (TYLCD) caused by Tomato yellow leaf curl virus (TYLCV) has been identified in Okinawa Prefecture, a subtropical region in Japan, for the first time in 2007. Infected tomato plants were collected from Tomigusuku City, Uruma City, Yomitan-son, and Nakijin-son on the main island of Okinawa. The complete nucleotide (nt) sequence of the TYLCV-Israel[Japan:Tomigusuku:2007] (TYLCV-IL[JR:Tom:07]) isolate obtained from Tomigusuku was determined. The sequence comparison with four representative TYLCV isolates in Japan showed that TYLCV-IL[JR:Tom:07] was most closely related to TYLCV-Israel[Japan:Tosa:2005] (TYLCV-IL[JR:Tos:05]), a member of the Israel strain of TYLCV (TYLCV-IL). The phylogenetic relationship analyses were performed based on determined partial nucleotide sequences of approximately 1,400 nt of 14 other isolates collected from 7 distinct locations. All the Okinawa isolates were separated into the cluster including TYLCV-IL[JR:Tos:05] and at least 2 distinct isolates of the TYLCV-IL were introduced onto the main island of Okinawa. These results indicated that the introduction of TYLCV into Okinawa might have been caused by domestic transportation of infected plants.