Recently, we reported that diploid sequence type (DST) 140 was a predominant type of Candida tropicalis among isolates with fluconazole minimum inhibitory concentrations (MICs) >or=64 microg/ml collected in the Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY) in 1999. To determine if DST140 persists in Taiwan, we have used multilocus sequence typing to characterize the genetic profiles of 31 resistant isolates (MICs >or=64 microg/ml), together with 19 susceptible isolates (MICs <or=16 microg/ml) collected in TSARY 2006. Among the 50 isolates, 33 distinct DSTs were detected. Of the 31 resistant isolates, 11 (35.5%) belonged to two closely related DSTs (140 and 98), whereas none of the 19 susceptible isolates did (p = 0.004). The isolates belonging to DST140 and 98 were from different geographic regions instead of a restricted area. Thus, our data show temporal and spatial transmission of C. tropicalis clones with high fluconazole MICs in Taiwan from 1999 to 2006.