Abstract: Dermatophytes and Candida are the most common sources of human fungal infections. Identification of dermatophytes and Candida using the traditional methods is sometimes problematic because of atypical microscopic or macroscopic morphology. The aim of this study was to identify and evaluate the genetic relationship among 6 species of dermatophytes and 3 species of yeasts isolated from Egyptian and Libyan patients with skin mycosis using three molecular techniques (RAPD, ISSR and RFLP) and isozyme profiles. Each species was represented by two isolates, one from Egyptian patients and the second from Libyan. Random amplified polymorphic DNA (RAPD) in which four random 10-mer primers and two Inter-Simple Sequence Repeat (ISSR) primers were used to amplify the DNA fragments of target fungi. Restriction Fragment Length Polymorphism (RFLP) in which two universal primers (ITS1 and ITS4) were used to amplify the Internal Transcribed Spacer (ITS) regions of the ribosomal (rRNA) gene in fungal isolates followed by digestion with HinfI and HaeIII endonucleases. Results of RAPD and ISSR markers revealed 78.7% Genetic Similarity (GS) between M. canis and other tested fungi reflecting a relatively longer genetic distance from other isolates of dermatophytes and yeasts. C. krusei and C. tropicalis were closely related showing 93.3% GS. C. albicans showed 90.9% similarity with other species of Candida. E. floccosum was easily separated from all Trichophyton species showing 87.3% similarity. Unique bands were displayed by certain fungi and can be taken as a positive marker for isolate identification and discrimination. RFLP technique revealed differences in the number (1-5) and size (8-378 base pairs) of DNA fragments depending on the fungal isolate and restriction enzyme used. Within each fungal species, different isolates of dermatophytes and Candida from Egypt and Libya showed close relationship. Seven isozyme systems were studied to detect the gene expression and genetic variability among the different isolates of dermatophytes and Candida.