OBJECTIVES: The genetically diverse parasite populations have greater potential to resist antimalarials, vaccines, and host immune responses. So, it is of key importance to know how they are associated with disease manifestation among humans. The present study is designed to evaluate whether the genetic diversity of Plasmodium falciparum has any role in altering the performance of malaria rapid detection kit. METHODS: We first examined the incidence pattern of all four malarial species using 18S rRNA gene among northern Indian malaria cases. Subsequently, we compared genetic variance of pfhrp2 gene among different malarial populations. Phylogenetic and principal component analysis (PCA) was carried out based on the frequencies of Plasmodium species. Subsequently the multi-dimensional scaling analysis was performed to evaluate the genetic similarities, and distances among studied populations. RESULTS: A total 561 febrile patients with unknown reason of pyrexia were included in the study while screening 2168 patients. 18S rRNA and Pfhrp2 gene was amplified in 78 and 45 samples respectively. Among them 78 (78/561, 13.9%) patients had Plasmodium infection. P. falciparum and P. vivax was diagnosed among 47 (60.2%) and 28 (35.9%) and 3 (3.8%) patients respectively. Eight types of Pfhrp2 repeats were found among the plasmodium strains of northern India. PCA findings supported the genetic diversity and phylogenetic data. Proportion of total diversity was highest for P. falciparum in the total subpopulation (ΔS/ΔT). CONCLUSIONS: Higher level of pfhrp2 sequence diversity leads to higher transmission intensity as well as the sequence variation may alter the sensitivity of rapid detection tests.