The present study explores the mycoflora associated with stored, Triphala churn and its raw material. Total 106 stored fruits and 68 powdered samples have been analysed for their fungal and mycotoxin association, if any. Results revealed that total 21 fungal species belonging to 11 different genera, in which eight species were only from genus Aspergillus, four from Penicillium and single species of each Helminthosporium, Curvularia, Alternaria, Geotrichum, Fusarium, Rhizopus, Paecilomyces and Syncephalastrum was recorded. About 97.36% of Triphala churn samples, 94.66% dried fruits and 89% powdered samples were found contaminated with various fungi. About 73.68% Triphala churn, 50% fruits and 20.58% powdered samples were found contaminated with six mycotoxins namely, aflatoxin B1 and B2, aflatoxin G1 and G2, citrinin and sterigmatocystin. All the six mycotoxins were detected from the samples of fruits and powder, whereas, five mycotoxins were detected from Triphala churn samples. After PCR analysis of most frequently occurring fungal species with two universal fungal primers ITS-1 and ITS-4, band pattern obtained on agarose gel clearly differentiating the different fungal species. Seven frequently observed species of Aspergillus namely, A. niger, A. terreus, A. fumigatus, A. flavus, A. terreus, A. parasiticus, A. versicolor were tested for their aflatoxigenic nature with omt-1 and ver-1 gene specific primers and amplification products of 895 and 596 bp were obtained only from A. flavus and A. parasiticus which indicate as aflatoxigenic nature. Presence of species of Aspergillus and Penicillium and mycotoxins in Triphala churn and its ingredients could represent a threat to consumers health.