The honey of stingless bees creates an unfavorable environment for pathogenic microorganisms due to its low pH and high acidity, making it safe for human consumption. However, it is prone to the development of molds, yeasts, and lactic acid bacteria at a pH below 4.5. Therefore, in this study, the objective was to quantify molds and yeasts in stingless bee honey and identify the detected microorganisms. For this purpose, the mold and yeast load in Melipona bicolor honey was quantified using acidified potato agar, and the present yeasts were identified molecularly through genomic DNA extraction and amplification of the ITS region by PCR using the primers V9G and ITS4. Initial denaturation was at 94°C for 5 minutes, followed by 35 cycles of denaturation at 94°C for 30 seconds, annealing at 48°C for 30 seconds, extension at 72°C for 1 minute, and a final extension step at 72°C for 10 minutes. DNA sequencing was performed with the BigDye kit on the ABI3500 sequencer, again using the V9G and ITS4 primers. Preliminary yeast identification at the genus level was conducted using the NCBI online BLAST tool. No molds were observed in the samples, with the exclusive growth of yeasts with similar macroscopic characteristics observed in all samples, with counts ranging from 3.28 to 7.30 log CFU.mL^-1 in raw honey. The yeast was identified as belonging to the genus Starmerella. Although a high quantity of yeasts was observed in the analyzed honey, molecular analysis indicated that they were non-pathogenic microorganisms for humans and associated with stingless bees, highlighting a relevant symbiotic relationship between these insects and the microorganisms present in the honey.