Fungal spoilage in cultured dairy products causes consumer dissatisfaction, food waste, and financial losses. This study aimed to identify fungi in spoiled cultured dairy products and to explore loci besides the ITS rRNA gene region for fungal identification. From 154 spoiled products, 201 fungal isolates were identified, with Penicillium, Mucor, and Yarrowia being the most abundant genera. We also amplified ITS, β-tubulin, calmodulin, and translation elongation factor gene regions in 114 additional isolates related to cultured dairy products. The ITS region in over 98% isolates were successfully PCR amplified and Sanger sequenced. Discrepancies were found between fungal identities assigned by BLAST search and phylogenetic analysis. The majority (81.25%) of isolates could not be assigned to the species level according to phylogeny reconstructed with their ITS sequence. β-tubulin sequences were obtained for around 50% of isolates. BLAST searches with β-tubulin sequences misidentified some Candida and Geotrichum isolates as Penicillium and Mucor isolates as Yarrowia. Our findings highlight the need for using multiple loci and combining phylogenetic analysis with BLAST search for accurate fungal identification. Future research should optimize primers for additional loci to complement ITS.