Millions of superficial fungal infections are annually observed in humans and animals. The majority of these mycoses are caused by dermatophytes, a specialized group of filamentous fungi that exclusively infect keratinized host structures. Despite the high prevalence of the disease, dermatophytosis, little is known about the pathogenicity mechanisms of these microorganisms. This drawback may be related to the fact that dermatophytes have been investigated poorly at the molecular level. In contrast to many other pathogenic fungi, they grow comparatively slowly under in vitro conditions, and in the last decades, only a limited number of molecular tools have been established for their manipulation. In recent years, however, major promising approaches were undertaken to improve genetic analyses in dermatophytes. These strategies include efficient systems for targeted gene inactivation and gene silencing, and broad transcriptional profiling techniques, which have even been applied in sophisticated infection models. As a fundamental prerequisite for future genetic analyses, full genome sequences of seven different dermatophyte species have become available recently. Therefore, it appeared timely to review the available molecular tools and methodologies in dermatophyte research, which may provide future insights into the virulence of these clinically important pathogens.