Eight species of Aspergillus (A. hiratsukae, A. flavus, A. fumigatus, A. terreus, A. niger, A. sydowii, A. clavatus and A. flavipes) were found associated with clinical samples causing human diseases. The nonspecific symptoms and lack of rapid diagnostics is a major problem in treating patients suffering from invasive aspergillosis. Molecular markers based on RAPD primers and diversity in ITS region of 5.8S rRNA gene developed for rapid diagnosis facilitated early treatment of patient suffering from aspergillosis related disorders. Direct sequencing of amplified ITS products revealed significant single nucleotide polymorphism, which facilitated identification of pathogenic Aspergillus species associated with aspergillosis. The complete sequences of eight Aspergillus species were submitted to NCBI database, USA, which were assigned new Gen accession numbers EU515147 to EU515154 and now available in public domain for comparison.