Bovine ephemeral fever (BEF) is a vector-borne disease of cattle, spanning tropical and subtropical zones of Asia, Australia, and Africa, caused by Ephemerovirus of the Rhabdoviridae. Taiwan has had 3 BEF epizootics, occurring in 1989, 1996, and 1999, since the vaccination regimen was initiated in 1984, given once a year in the spring with a single-dose formaldehyde-inactivated vaccine using the 1983 isolate as the seed virus. This study evaluated the 1999 population immunity against BEF virus in Taiwanese dairy cows with a neutralization test and whether the recent BEF virus isolates have mutated significantly from the vaccine virus. In March 1999, before vaccination, 94% of the animals studied were already seropositive, suggestive of an endemic or persistent infection from the previous year. By June 1999, when 51% of herds had been vaccinated, the antibody level rose, and by September 1999, the serum-neutralizing antibody (SNA) level fell to a minimum, preceding the outbreak of BEF in October 1999, during which the antibody levels of vaccinated cows continued to decline while those of unvaccinated cows rose sharply. The results suggest that, in 1999, vaccine-induced immunity was partially protective against BEE Because the current single-dose vaccination regimen resulted in minimal population immunity by September, a booster vaccination given in late summer may be advisable for future disease control. Analysis of the glycoprotein gene of Taiwanese isolates between 1983 and 1999 showed a 97.4-99.6% homology, with an alteration of 4 amino acids in antigenic sites G1, G3b, and G3c. Phylogenetic analysis of Taiwanese isolates revealed at least 2 distinct clusters: the 1983-1989 isolates and the 1996-1999 isolates. Both were distinct from 2 Japanese strains and the Australian BB7721 strain. Thus, at least 2 distinct BEF viruses, which had diverged before 1983, existed in Taiwanese dairy cows.