Malassezia is a commensal that sometimes become pathogenic under the influence of diverse factors. Several species of Malassezia are difficult to culture, making traditional methods of identification challenging. The problem with molecular typing of Malassezia in association with seborrheic dermatitis/dandruff (SD/D) arises due to the unavailability of these fastidious yeast cultures. The aim of the study was to investigate the association between fluorescent amplified fragment length polymorphism (FAFLP) genotypes, disease state (SD/D), and the geographic distribution of M. globosa, M. restricta and M. arunalokei. In total 154 isolates representing M. globosa (n=85), M. restricta (n=55), and M. arunalokei (n=14) from lesional/non-lesional areas of SD/D patients and healthy controls residing in the rural (n=77) and urban (n=77) areas of northern India were included. A strategy based on the FAFLP methodology was developed using two endonuclease enzymes (EcoRI and HindIII). M. globosa, M. restricta, and M. arunalokei formed eleven, three, and two FAFLP clusters respectively. Disease-specific strains of M. restricta and M. arunalokei preferentially tend to cause SD/D. M. restricta and M. arunalokei showed less genetic variation. M. globosa showed higher genetic diversity. FAFLP clusters revealed the existence of geographically specific strains in M. restricta, M. arunalokei, and M. globosa. Our findings suggest that certain Malassezia strains are not only disease-specific but also geographically distinct.