Understanding the genetic diversity and transmission dynamics of Plasmodium falciparum , the causative agent of malaria, is crucial for effective control and elimination efforts. In some endemic regions, malaria is highly seasonal with no or little transmission during up to 8 months, yet little is known about how seasonality affects the parasite population genetics. Here we conducted a longitudinal study over 2.5 year on 1516 participants in the Upper River Region of The Gambia. With 425 P. falciparum genetic barcodes genotyped from asymptomatic infections, we developed an identity by descent (IBD) based pipeline and validated its accuracy using 199 parasite genomes. Genetic relatedness between isolates revealed a highly recombinatorial genetic diversity, suggesting continuous recombination among parasites rather than the dominance of specific strains. However, isolates from the same household were six-fold more likely to be genetically related compared to those from other villages. Seasonal patterns influenced genetic relatedness, with a notable increase of parasite differentiation during high transmission. Yet chronic infections presented exceptions, including one individual who had a continuous infection by the same parasite genotype for at least 18 months. Our findings highlight the burden of asymptomatic chronic malaria carriers and the importance of characterising the parasite genetic population at the community-level. Most importantly, ‘reactive’ approaches for malaria elimination should not be limited to acute malaria cases but be broadened to households of asymptomatic carriers.