Purpose Little knowledge is available regarding the possibility of conversion of agro wastes through cultivation of indigenous wild strains of Flammulina velutipes and interactions between substrate composition and F. velutipes strain. This study was thus conducted to compare effects of several locally available agro wastes on the growth characteristics of Iranian wild and cultivated strains of F. velutipes. Methods Nine different substrate compositions were made based on sawdust, sugarcane bagasse, soybean meal, wheat bran, and wheat straw. The main and simple effects of the substrate compositions as well as interactions between mushroom strain and substrate were comparatively determined. Results While significant interactions between substrate and mushroom strain were observed (p \ 0.05), the mixtures of wheat straw and wheat bran enriched with soybean meal or sawdust highly supported vegetative and reproductive growth of both strains (p \ 0.05). Amongst the selected formulations that generated biological efficiencies more than 100 %, the substrate containing 40 % wheat straw ? 40 % sawdust ? 18 % wheat bran gave an outstanding biological efficiency of 265 % for the cultivated strain (p \ 0.05). Amid the serious environmental problems caused by the accumulation of sugarcane bagasse in Iran, this study also showed that both wild and cultivated F. velutipes can effectively be grown on sugarcane bagasse supplemented with wheat bran. Conclusion The selected agricultural wastes evaluated in this study may be suggested as new formulations for growing either indigenous or cultivated strains of medicinal mushroom F. velutipes.