Red chilli (Capsicum annuum L.) is a major crop of Pakistan. Sindh contributes 85% of its production and a small town “Kunri” is one of the largest centres for red chilli production in Asia. Red chilli is a major food ingredient and is utilized for the production of essence, pungency and red color. It is an excellent source of vitamin C and has several medicinal uses. The overall production of red chilli has decreased during the years 2006-2007. One of the main reasons for this decline is mycotoxin contamination. Contamination by mycotoxins in the red chilli crop drastically reduces its quality, due to which Pakistani red chilli is unable to enter in the world market and has been banned by European Union Food Authorities, which led to the decrease in export and production. Mycotoxins are a chemically diverse group of fungal metabolites that have a wide variety of toxic effects. The most serious and toxic example are the Aflatoxins (B1, B2, G1, G2) produced by Aspergillus flavus and A. parasiticus. Aflatoxin B1 is considered a major cause of liver cancer. The present study was planned to develop an integrated approach for the management of mycotoxin contamination in red chilli. For this purpose, available germplasm was evaluated to determine the resistance level of red chilli varieties against mycoflora and production of mycotoxins. The mycoflora were isolated by employing standard techniques; associated mycotoxins were analyzed by chromatographic techniques; different antagonistic bioagents and plant diffusates were tested in-vitro for their effectiveness in managing the mycotoxins and mycotoxin producing fungi. The highly susceptible variety „Nagina‟ was subjected to crop management trials in the greenhouse. Firstly, different irrigation levels were evaluated; which have been reported to induce significant reductions in 1 2 toxins. Secondly, different species of yeast like Saccharomyces cerevisae, S. bayanus, S. postoranus and their doses were applied at flowering stage of crop. Finally, the best treatment from these individual trials was incorporated in an integrated mycotoxin management experiment. The significance of each treatment in trials was evaluated by detection and quantification of mycotoxins, estimation of yield components (fresh weight, dry weight, number of pods), nutritional profile and seed viability of produce. At this stage, the formulation of plant diffusates and bio agents with highest proficiency in the in-vitro management trial were applied to chilli pods and pre and post-application status of mycotoxins were recorded. This study provides a record of the mycoflora and mycotoxins associated with various varieties of red chilli. Most importantly, it provides the resistant/tolerant locally available red chilli cultivars (Kunri & Drooping type) which were less contaminated. In addition, the use of Saccharomyces species during pre-harvest and Lactobacillus rhamnosus at the post-harvest stage were some major findings of this study. Finally, the integration of best pre and post-harvest treatments was the most useful strategy for the management of mycotoxins in red chilli. This work provides better and more cost effective technology for farmers to produce high quality toxin free chillis which will not only increase the demand for Pakistani products in international markets but will also become the source of enhanced foreign exchange and farmer income.