Two genotypes of foot-and-mouth disease virus serotype A were identified as the cause of disease outbreaks in Turkey during 1996-2004, while serotype O strains, identified during the same period, seem to represent an evolutionary continuum, and Asia1 strains were only rarely identified. The data presented are concordant with the conclusion that serotype A strains are repeatedly introduced to Turkey from the east and circulate only transiently in farming communities, while type O strains persist and re-emerge from endemic areas of Turkey. The co-circulation of strains belonging to two A genotypes for 6 years, as observed in the present study, is a remarkable difference compared to previous decades in which only one A genotype was transiently circulating, successively being replaced by others. This co-circulation was observed in spite of enforcement countrywide of biannual vaccination of more than 50% of the cattle during the same period. Mean r(1) values of 0.70 +/- 0.19 and 0.39 +/- 0.04 found for A96 and A99 isolates, respectively, compared to the A96 vaccine component reveal antigenic differences but also imply that the vaccine in use in Turkey should provide protection against both genotypes. It is suggested that further studies to reveal the nature of the difference in epidemiological dynamics of type A and type O strains might lead to an understanding of the measures required to control foot-and-mouth disease in islands of persistent circulation.