A study was undertaken to find the molecular and physiological variability in Aspergillus awamori strains isolated from different agroclimatic zones of Karnataka. A. awamori strains from different agro climatic zones were isolated, identified and confirmed using standard synaptic keys. Plant growth response studies using tomato as host were conducted. The heights of plants were found to increase steadily with number of days. In plants inoculated with A. awamori isolates, the height, number of leaves, fresh and dry weight of roots and shoots, P content and total sugars remained higher than the uninoculated plants. Isolate 1 performed well compared to other isolates. In the protein profile of different A.awamori isolates, Rm values of the bands were ranging from 0.006 to 0.54. Almost common bands were observed among the isolates 1, 2, 3 and 4 except some bands, but they differed only in their intensity. Similarity index was more between isolates 1 and 4; 2 and 5; and 4 and 5 (0.94) whereas it was less between isolates 1 and 9, 1 and 10, 5 and 10, 6 and 9, 6 and 10, and 8 and 10 (0.44). The results suggest that protein profiles data can closely separate isolates from different zones.