This work demonstrates the antimycotic activity and structural damage of stingless bee propolis against Malassezia pachydermatis,causative agent of canine otitis.Two propolis ethanolic extracts(EEP) derived from the stingless bees, Scaptotrigona mexicana and Tetragonisca angustula were tested against three clinical strains of Malassezia pachydermatis and one of reference (ATCC 14522). Each ethanolic extract of propolis was analyzed by Gas Chromatography – Mass Spectrometry(GC-MS). Antimycotic activity was evaluated by plate microdilution. To evaluate the induced changes in yeasts, by fluorescence microscopy, stains were performed with chalcofluor white and propidium iodide. For both propolis, sesquiterpenes were the main components determined by GC-MS. Minimum inhibitory concentration (MIC) of 32 mg/mL and a minimum fungicidal concentration of 64 mg/Ml were determined in both extracts. EPP of Scaptotrigona mexicana and Tetragonisca angustula caused significant damage to yeast morphology. Propidium iodide penetration was observed, indicating damage to the yeast and with calcofluor-white stain, only morphology deformation was observed..The antimycotic activity and structural damage of propolis from Scaptotrigona mexicana and Tetragonisca angustula against Malassezia pachydermtais was demonstrated .This probably being the first scientific report that demonstrates structural damage in Malassezia pachydermatis of Mexican stingless bee propolis