Malaria is the fourth leading cause of deaths among communicable diseases in Pakistan. Federally Administered Tribal Areas (FATA), Baluchistan and Khyber Pakhtunkhwa provinces have one of the highest Annual parasite incidence (API) within the country. Present study aimed at elucidating epidemiology and comparing performance of several diagnostic procedures in Bannu, a highly endemic district (API of 1.6-3.5 per 1000) of Khyber Pakhtunkhwa. The aim of this PhD project was to generate current information on parasite prevalence through active antigen detection and also investigated the risk factors of malaria. In addition, genetic diversity among existing P. vivax strain was also investigated. A total of 2033 blood samples of suspected cases were collected and processed through three diagnostic technique including microscopy, RDT and parasite species specific PCR. A questionnaire was administered to collect household and individual based information to determine the potential risk factors of malaria. The present study was performed from 2012 to 2013. Samples were collected from suspected individuals of rural and urban areas visiting laboratory. Microscopy and Rapid Diagnostic Test was used on the spot for detection of Plasmodium species. A total of 2033 individuals were recruited, of whom 21.1% (N=429) were positive for malaria by at least one method. Overall, positivity detected by PCR was 30.5% (95/311) followed by 17.7% by microscopy (359/2033) and 16.4% by RDT (266/1618). Plasmodium vivax (16.9%, N=343) was the detected as the dominant species followed by Plasmodium falciparum (2.3%, N=47) and mixed infections (1.2%, N=39). Microscopy and RDT (Cohen''s kappa k=0.968, 15 p=<0.0001, McNemar test p=0.069) v displayed significant agreement with each other, suggesting that RDT may be a useful alternative to microscopy in the field. Satisfactory health, sleeping inside room, presence of health care facility in vicinity (at an accessible range from home), living in upper middle class and in concrete houses significantly reduced malaria risk. On the other hand, low literacy level, presence of domestic animals indoors and a diagnosis recommended by clinician increased the disease risk. Mitochondrial genome sequencing of Plasmodium vivax revealed the existence of significant number of SNPs in coding and non-coding region of the genome while population structure analysis shown the presence of strain which are closely related to the strains of other regions. Population genetic study identify the significant mutation in the genome. It also identifies the large evolutionary distance between Pakistani and other regions P. vivax strains. This data will help to provide beneficial and up-to-date information to manage control activities in the study area. Appropriate management of identified risk factors can benefit in reducing the prevalence of malaria in Bannu and its peripheries.