Canine seborrheic dermatitis (SD) is the common chronic relapsing inflammatory skin condition; triggered by susceptible host-mediated immune responses and opportunistic yeast infection. Characterization of canine skin yeast diversity, antifungal susceptibility determination and uncovering of underlying immune responses on SD progression may take a step forward in pathogenesis of canine SD. Diversity and population size of canine skin yeasts were characterized corresponding to skin conditions and stages of SD; healthy, primary SD (PSD) and secondary SD (SSD). Malassezia pachydermatis and Candida parapsilosis were majority population of canine skin yeast flora. The co-colonization of these yeasts in large amount and frequency associated with stages of SD. There were no significant differences in the yeasts resistant rates between SD and healthy dogs. Ketoconazole and itraconazole were still efficacious for M. pachydermatis but a high rate of KTZ resistant was reported in C. parapsilosis. Immunoglobulin G subclass could differentiate the responsive patterns on each progression of disease and immunodominant antigens to IgG subclasses were identified and may reflect the important components inducing or control of the disease.