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Background  Malaria is still a serious public health problem on Bioko Island (Equatorial Guinea), although the number of annual cases has been greatly reduced since 2004 through the Bioko Island Malaria Control Project (BIMCP). A better understanding of malaria parasite population diversity and transmission dynamics is critical for assessing the effectiveness of malaria control measures. The objective of this study is to investigate the genetic diversity of  Plasmodium falciparum  populations and multiplicity of infection (MOI) on Bioko Island 7 years after BIMCP.    Methods  A total of 181 patients with uncomplicated  P. falciparum  malaria diagnosed with microscopy were collected from Bioko Island from January 2011 to December 2014. Parasite DNA was extracted using chelex-100 and species were identified using a real-time PCR followed by high-resolution melting.  Plasmodium falciparum msp1  and  msp2  allelic families were determined using nested PCR.    Results  Three  msp1  alleles (K1, MAD20, and RO33) and two  msp 2 alleles (FC27 and 3D7) were analysed in all samples. In  msp1 , the MAD20 allelic family was predominant with 96.69% (175/178) followed respectively by the K1 allelic family with 96.07% (171/178) and R033 allelic family with 70.78% (126/178). In  msp2 , the FC27 allelic family was the most frequently detected with 97.69% (169/173) compared to 3D7 with 72.25% (125/173). Twenty-six different alleles were observed in  msp1  with 9 alleles for K1, 9 alleles for MAD20 and 8 alleles for R033. In  msp2 , 25 individual alleles were detected with 5 alleles for FC27 and 20 alleles for 3D7. The overall MOI was 5.51 with respectively 3.5 and 2.01 for  msp1  and  msp2 . A significant increase in overall MOI was correlated with the age group of the patients ( P  = 0.026) or parasite densities ( P  = 0.04).    Conclusions  The present data showed high genetic diversity and MOI values among the  P. falciparum  population in the study, reflecting both the high endemic level and malaria transmission on Bioko Island. These data provide valuable information for surveillance of  P. falciparum  infection and for assessing the appropriateness of the current malarial control strategies in the endemic area.

Genetic diversity and allele frequencies of Plasmodium falciparum msp1 and msp2 in parasite isolates from Bioko Island, Equatorial Guinea