Mushroom is considered a sensitive crop as it requires special care for contolling insect pests damages especially through phorid (Megaselia halterata) and sciarid (Lycoriella auripila) flies during March-November, creating cultivation problems and serious threat for mushroom industry in Pakistan, Sometime severe infestation of phorid and sciarid flies result into the total crop collapse. Thus, present study was planned (1) to evaluate the comparative efficacy of different insecticides (Trichlorphon, Malathion, Spinosad, Endosulfan, Deltamethrin, Spintoram, Imidacloprid, Diafenthuron and Permethrin) against these flies, (2) to evaluate the potential of six botanical (Neem nut. Neem leaves, Eucalyptus leaves, Nerium indicum leaves, Castor bean leaves and Tobacco leaves), (3) to determine the effectiveness of cultural/physical control (Light traps, Screening mesh, Hygiene and Temperature) and finally, (4) the integration of all these control measures in a compatible manners during three successive years of study. All the treatments were evaluated on the basis of reduction in adult of mushroom flies emergence (RAE), mushroom damage rate (MDR) in percentage and yield in three successive growing periods. Six insecticides viz., Trichlorphon, Malathion, Spinosad, Deltamethrin, Spintoram and Permethrin, out of nine, caused 77.42% to 90% mortality of 3 rd instar larvae of phorid and sciarid fly under lab condition, while 73% to 88% in mushroom houses. Four plant extracts [Neem nut, Neem, Tobacco and Kanair (Nerium indicum)] out of six caused 41% to 72% mortality of 3 rd instar larvae of phorid and sciarid fly under lab conditions, while 40% to 68% in mushroom houses. Pink colour flap light trap trapped maximum average mushroom flies per week (85.50) followed by yellow (57.00), blue (33.95) and white (19.45), respectively. Screening mesh and hygiene proved best reducing adult emergence up 51.18% and 45.79%, respectively. Integration of insecticides with plant extracts proved very effective against mushroom flies (phorid and sciarid). It controled the adult emergence about 90.82 to 92.44% in mushroom house. In the same way, integration of chemical cultural and control controlled mushroom flies up to 91.72% and 93.34% in mushroom houses. While, the integration of plant extracts and cultural methods controlled the phorid and sciarid fly up to 77.57% and 76.51% respectively, in mushroom houses.