Molecular surveillance is pivotal to fully grasp the impact of malaria control interventions in high-transmission settings. However, the majority of Plasmodium falciparum infections in these regions are asymptomatic with low gDNA and are multiclonal. Molecular tools have been created to monitor P. falciparum populations yet are seldom validated on the reservoir of asymptomatic infection and in high-transmission settings. We present a population genetic study that compares the performance of a biallelic 20 single nucleotide polymorphisms (SNPs) barcode and 10 polymorphic microsatellite markers on asymptomatic P. falciparum isolates in a high-seasonal transmission setting in northern Ghana, West Africa. P. falciparum multilocus infection haplotypes were constructed from SNPs and from microsatellites for the same isolates across two age-stratified cross-sectional surveys before and after an indoor residual spraying (IRS) intervention which led to a >90% reduction in transmission intensity and 35.7% reduction in the P. falciparum prevalence. The multiplicity of infection (MOI) and genetic diversity parameters were compared between the two markers. Strikingly, 10 SNP loci (50%) had minor allele frequencies ≤10% in the population at both time points (i.e., pre- and post-IRS). Using THE REAL McCOIL method to estimate MOI from the SNP-genotyped isolates, we found that it could not reliably estimate isolate MOI when compared to other methods, including msp2 typing. Population genetic analyses of the SNP infection haplotypes showed low expected heterozygosity, high genetic relatedness, and the presence of clones in the population. However, microsatellite analysis revealed that infection haplotypes were highly diverse with low genetic relatedness, as all multilocus haplotypes were unique. This SNP barcode originated from surveillance in Senegal and yet has proven to be unsuitable for this location in northern Ghana. These data posit that this proposed SNP barcode is not suitable to assess MOI or genetic diversity in this high-transmission setting. This leads us to question the utility of SNP barcode in high-transmission if it cannot deal with multiclonal infections and must be customised for parasite populations at local geographic scales. This study further highlights the utility of microsatellites with multiple alleles per locus as a neutral marker in high-transmission settings.