Seven seed samples were collected from major ajwain growing areas of Rajasthan to prove the pathogenicity of fungi isolated from seed samples viz., A, B, C, D, E, F and G. All the fungi reduced seed germination and seedling vigour by causing pre (seed rot) and post emergence mortality (seedling blight, wilting and yellowing). Amongst these fungi viz., Aspergillus flavus, Aspergillus niger, Aspergillus ochraceous, Drechslera australiensis and Fusarium sporotrichioides proved to be highly virulent caused high per cent pre- and post emergence mortality and per cent seedling showing symptoms on inoculation the seeds, seedling and also by mixing in soil. The deteriorative effect of seed mycoflora on volatile oil contents of ajwain seeds, separate inoculations were made with seven different mycoflora. Seed inoculated with Drechslera australiensis showed increase in per cent volatile oil content. Seed inoculated with rest of the fungi viz., Aspergillus flavus, A. niger, A. ochraceous, D. australiensis, F. sporotrichioides, Rhizopus oryzae and Trichoderma viride showed reverse/equal in per cent volatile oil contents of seeds.