In order to study the antifungal activity of propolis ethanol extracts (PEE) from Apis mellifera bees from Mexico we used optical microscopy and we were able to see that PEE induced inhibition of germ tube formation of C. albicans. Ultrastructural findings were seen using transmission electron micrographs of ultrathin sections of Candida albicans revealed that these cells suffered vacuolization, increased formation of storage granules as well as alteration and disruption of the outer structures of yeast, with release of intracellular material. In order to describe the molecular mechanism of action, we evaluate gene expression. We were able to identify some over- and under-expressed genes. ADH1 y PIK1 genes were under-expressed in a manner dependent on concentration and exposure time. On the other hand, our team has determined the chemical profile of several Mexican propolis, with interesting results as the diversity of content and different levels of antifungal and antibacterial activities.