In Thailand, four systemic fungicides-carbendazim (Car), azoxystrobin (Azo), difenoconazole (Dif), and penthiopyrad (Pen)-are commonly used to control soybean anthracnose caused by ; however, the pathogen has developed resistance. From 2019 to 2020, fungicide resistance in from fields in Chiang Rai and Chiang Mai was monitored. In tests of 85 isolates for resistance to multiple fungicides, 15.3% were CarAzo, 34.1% were triple resistant (CarAzoDif or CarAzoPen), and 50.6% were CarAzoDifPen. Surprisingly, all isolates tested had lost their sensitivity to one or more of the fungicides tested. The carbendazim-resistant isolates carried a point mutation in the β- gene at codon 198 (E198A) or 200 (F200Y), and all azoxystrobin-resistant isolates had a mutation in the cytochrome gene at codon 143 (G143A) or 129 (F129L). Moreover, a novel mutation at codon 208 (S208Y) in the gene encoding succinate dehydrogenase subunit B was detected in all of the isolates highly resistant to penthiopyrad. No mutation linked with difenoconazole resistance was detected in the genes encoding cytochrome P450 sterol 14α-demethylase. To the best of our knowledge, this is the first report of isolates resistant to multiple fungicides and serves as a warning to take measures to prevent the occurrence and distribution of these multiple-fungicide-resistant populations in soybean fields.