In Uganda, wild mushrooms are mainly collected during the rainy season and valued as a traditionally nutritious food by the rural poor. However, their nutritional attributes have not been adequately studied and documented. Comparative nutrient composition of five wild edible mushroom species was determined, namely: P. tenucuilus, T. tyleranus, T. clypeatus, V. speciosa and T. microcarpus of sub-humid and humid agro-ecological zones. Standard analytical techniques following the AOAC were used for proximate and mineral contents determinations. Vitamins determination followed the established standard protocols of the laboratories where the analyses were conducted. Combined use of nutrient concentration and scores were used to compare the level of the contents in the mushroom species. Significant differences (p < 0.05) in nutrient values were demonstrated between and among the mushroom species obtained from the two agro-ecological zones. On dry weight basis, all proximate compositions were high in mushroom species obtained from the humid zone with exception of the total carbohydrates and energy values. Irrespective of the source of the mushrooms, significant amounts were demonstrated in protein, dry matter, ash and total carbohydrates ranging between 11.56–27.42%, 82.34–99.76%, 10.79–16.87%, and 37.12–61.05%, respectively. In comparison with recommended dietary daily intakes, the K, P, Se, Mn, Cu and Fe contents were relatively high with low Ca, Mg, Zn and Na. Thiamin, folic acid, vitamin C, and niacin levels were high but below the recommended FAO references. Considering mushrooms from different agro-ecological zones, significant differences (p < 0.05) were observed in all mushroom species in P except in T. clypeatus, T. tyleranus, T. microcarpus and T. clypeatus in potassium, T. clypeatus and T. microcarpus in Mg. Mushrooms from humid agro-ecological zones had relatively high overall mineral and vitamin supply potential. In conclusion, consumption of these mushrooms should be encouraged in supplementation of the staple food of the poor people. Hence, solving malnutrition problems in children, pregnant mothers, and the immune compromised patients such as the HIV/AIDs.