The nucleotide sequence of Epstein-Barr virus (EBV) nuclear antigen (EBNA)-2 and EBNA-3B regions of an EBV-2 isolate in Japan was analyzed. The deduced amino acid sequences of EBNA-2 and EBNA-3B of the isolate and a prototype EBV-2 strain AG876 were identical, but the number of the repeated sequence in EBNA-3B was variable as that of IR-3 in EBNA-1. The remarkably well-conserved sequence seems to suggest that the structure of the EBNA-2 and EBNA-3B genes of EBV-2 is crucial for their function in virus replication.