Fruit flies (Diptera: Tephritidae) having economic importance because of pest attacking throughout the world on various fruits and vegetables. The genus of fruit flies; Bactrocera are serious pests of fruits and vegetables, hence the studies were carried out to find out the level of fruit fly infestation, comparison of fruit fly attractants and molecular identification of fruit fly species in Khyber Pakhtunkhwa (KP). The trials were laid out in randomized complete block design, replicated three times on various fruits and vegetables in KP during 2010 and 2011. The experimental studies were carried out on Guava at Kohat, Peach at Swat and Bitter gourd at Charsada. The data of infestation were recorded on counting healthy and infested fruits and vegetable randomly. Findings of the study showed that fruit fly infestation gradually gained from mid April and reached to its peaks in mid August and then dropped till mid November in Guava orchards. In case of Peach orchards, fruit fly infestation varied during the study periods in both the years (2010 & 2011). The infestation increased from mid April and gained its peaks in August and thereafter started declined till October. In similar way, fruit flies infestation in Bitter gourd at Charsada reached to highest percentage in months of August, drastically decreased and the lowest records were in the month of November. It was concluded that the presence of fruit fly was recorded in all the three orchards throughout their crop seasons and this window is considered a critical one in the management of fruit fly. The findings of three different attractants i.e, Methyl eugenol (M.E), Cue lure (C.L) and PPr-Product (locally made protein/yeast autolysate based) showed that significant variation for the captured of fruit flies among attractants and observational dates in Guava, Peach and Bitter gourd orchards. M.E trapped more fruit flies as compared PPr-Product and C.L traps in Guava and Peach orchards whereas higher number of fruit flies was captured by PPr-Product as compared to both C.L and M.E traps in Bitter gourd orchards. Higher capture of Bactrocera zonata and Bactrocera dorsalis in Guava and Peach orchards was recorded by M. E whereas C.L attracted more Bactrocera. cucuribitae as compared to M.E traps for Peach, Guava and Bitter gourd orchards. More number B. zonata and B. dorsalis captured by PPr-Product in Bitter gourd. The PPr-Product traps were found more effective against all three types of female adults flies whereas M.E traps captured more B. zonata and B. dorsalis while C.L captured more male adults of B. cucurbitae in xiPeach, Bitter gourd and Guava orchards. For molecular analysis of five major Tephritids fruit fly species (B. zonata, B. dorsalis, B. cucurbitae, Bactrocera tau and Myiopardalis pardalin) the mitochondrial cytochrome C oxidase (COI) gene was amplified using primers previously described for the conserved region and the amplified products were subjected to RFLP analysis and sequencing. Analysis of the PCR-RFLP profile of COI gene using primers LCOI and HCOI and restriction enzymes (PstI, HincII, HaeIII, BamHI and SspI) revealed that the five different restriction enzymes could efficiently differentiate among the Five (05) major fruit fly species analyzed in this study. Furthermore, sequencing and phylogenetic analysis of fruit fly species based upon the COI gene revealed species-specific distinct evolutionary trends.