Malassezia spp. have rarely been reported in rodents and lagomorphs. In 2011, Malassezia cuniculi was described in two rabbits. Further microscopic studies showed M. cuniculi-like yeasts in more than 50% of samples from rabbits’ ear canals, but no isolation was made. The present study details the presence of Malassezia spp. and tries to typify it from ear canals of healthy rabbits. Seventy-eight half-breed rabbits from rural farms and 98 companion dwarf rabbits from northern Italy were considered. A first attempt to screen ear swabs was performed by microscopic and cultural examination on Sabouraud Glucose Agar (SGA), modified Dixon Agar (mDA) and Leeming and Notman Agar (LNA). Additionally, ear swabs from eight further microscopically positive rabbits for M. cuniculi-like cells, were used for both isolation on LNA medium and nine of its variants and for DNA extraction, PCR and sequencing. The microscopic observation of the swabs of the screened 168 rabbits highlighted the presence of yeasts in one or both of the external ear canals of 98 rabbits (58.3%). Rabbits used for meat production were more frequently diagnosed positive than pet rabbits (P = 0.001), and young ones were more often positive compared to rabbits older than 3 months (P = 0.027). No yeast growth was observed in culture. From the eight selected rabbits, Malassezia isolation failed both on LNA and on the modified mediums. Sequences of ~300 bp fragments of 18s rDNA, obtained by PCR from swabs, showed 99.9% identity with Malassezia phylotype 131 described from human ear canals. As Malassezia-like yeasts have been observed in more than half of the examined population, its colonization of ear meatus can be considered as physiological in rabbits. The results outline how much remains to be discovered on Malassezia as a component of the skin mycobiota of rabbits and that the use of the culture examination alone is not the best choice to detect Malassezia-like yeasts in rabbits.