Objectiv e To analyze the imported Equatorial Guinean Plasmodium falciparum drug resistance gene polymorphisms in Henan Province, and provide a reference for the treatment of imported P. falciparum infections. Methods The medical records and peripheral blood samples were collected from the imported P. falciparum malaria cases original from Equatorial Guinea in Henan Province from 2012 to 2019. The P. falciparum genomic DNA was extracted and the P. falciparum genes, including Kelch 13-propeller (PfK13), chloroquine resistance transporter (Pfcrt), multidrug resistance 1 (Pfmdr1), dihydrofolate reductase (Pfdhfr) and dihydropteroate synthase (Pfdhps), were amplified by nested PCR. Bidirectional sequencing of the secondary PCR products was performed after agarose gel electrophoresis. The obtained sequences were aligned with the corresponding reference P. falciparum 3D7 strain genomes by MEGA7 software. The reference genomes were obtained from the GenBank (GenBank accession numbers: PF3D7_1343700, PF3D7_0709000, PF3D7_0523000, PF3D7_0417200 and PF3D7_1324800 respectively). The data were analyzed by SPPS 21.0 software. Results A total of 1 522 imported malaria cases were reported in Henan Province during 2012 to 2019, including 117 cases imported from Equatorial Guinea. Among the 117 cases, 97 cases were infected with P. falciparum, 16 cases were infected with P. ovale, 1 case was infected with P. vivax, 1 case was infected with P. malariae, 1 case was mixed infected with P. falciparum and P. malariae and 1 case was mixed infected with P. falciparum and P. ovale. The PfK13 gene was successfully amplified from 91 P. falciparum samples and the mutant prevalence was 8.8% (8/91). The non-synonymous mutation sites were M476I mixed type (mixed), A481V mixed, A564E mixed, P574L mixed, A578S, V589I and N609I mixed respectively. The synonymous mutation sites were G625G, N664N and C469C respectively. The Pfcrt gene was successfully amplified from 91 P. falciparum samples and the mutant prevalence was 18.7% (17/91). Three Pfcrt haplotypes were identified, including wild-type C₇₂V₇₃M₇₄N₇₅K₇₆ (81.3%, 74/91), mutant C₇₂V₇₃I₇₄E₇₅T₇₆ (12.1%, 11/91) and mixed-type C₇₂V₇₃M/I₇₄N/E₇₅K/T₇₆ (6.6%, 6/91). The Pfmdr1 gene was successfully amplified from 92 P. falciparum samples and the mutant prevalence was 77.2% (71/92). Three mutant codons were detected, including N86Y (41.3%, 38/92), Y184F (75.0%, 69/92) and D1246Y (1.1%, 1/92). The mutant prevalence of N86Y decreased from 68.8% in 2012 to 11.1% in 2016 (χ² = 11.58, P < 0.05). Five Pfmdr1 haplotypes were identified, including wild-type N₈₆Y₁₈₄D₁₂₄₆ (22.8%, 21/92), single mutants Y₈₆Y₁₈₄D₁₂₄₆ (1.1%, 1/92), N₈₆F₁₈₄D₁₂₄₆ (34.8%, 32/92), N₈₆Y₁₈₄Y₁₂₄₆ (1.1%, 1/92) and double mutant Y₈₆F₁₈₄D₁₂₄₆ (40.2%, 37/92). The Pfdhfr gene was successfully amplified from 90 P. falciparum samples and the mutant prevalence was 96.7% (87/90). Three mutant codons were detected, including N51I (91.1%, 82/90), C59R (93.3%, 84/90) and S108N (96.7%, 87/90). Five Pfdhfr haplotypes were identified, including wild-type N₅₁C₅₉S₁₀₈ (3.3%, 3/90), single mutant N₅₁C₅₉N₁₀₈ (2.2%, 2/90), double mutants I₅₁C₅₉N₁₀₈ (1.1%, 2/90), N₅₁R₅₉N₁₀₈ (3.3%, 3/90) and triple mutant I₅₁R₅₉N₁₀₈ (90.0%, 81/90). The Pfdhps gene was successfully amplified from 90 P. falciparum samples and the mutant prevalence was 97.8% (88/90). Six mutant codons were detected, including I431V (8.9%, 8/90), S436A (27.8%, 25/90), A437G (92.2%, 83/90), K540E (3.3%, 3/90), A581G (1.1%, 1/90) and A613S (2.2%, 2/90). Eight Pfdhps haplotypes were identified, including wild-type I₄₃₁S₄₃₆A₄₃₇K₅₄₀A₅₈₁A₆₁₃ (2.2%, 2/90), single mutants I₄₃₁A₄₃₆A₄₃₇K₅₄₀A₅₈₁A₆₁₃ (5.6%, 5/90), I₄₃₁S₄₃₆G₄₃₇K₅₄₀A₅₈₁A₆₁₃ (66.7%, 60/90), double mutants I₄₃₁A₄₃₆G₄₃₇K₅₄₀A₅₈₁A₆₁₃ (10.0%, 9/90), I₄₃₁S₄₃₆G₄₃₇E₅₄₀A₅₈₁A₆₁₃ (3.3%, 3/90), triple mutants V₄₃₁A₄₃₆G₄₃₇K₅₄₀A₅₈₁A₆₁₃ (8.9%, 8/90), I₄₃₁A₄₃₆G₄₃₇K₅₄₀G₅₈₁A₆₁₃ (1.1%, 1/90) and I₄₃₁A₄₃₆G₄₃₇K₅₄₀A₅₈₁S₆₁₃ (2.2%, 2/90). The Pfdhfr and Pfdhps genes were simultaneously successfully amplified from 89 P. falciparum samples and 84 (94.4%) samples had mutations in both genes. The most frequent mutation was the quadruple mutant I₅₁R₅₉N₁₀₈-G₄₃₇, which accounting for 64.0% among the gene mutations of Pfdhfr and Pfdhps. Conclusion Multiple mutant codons of PfK13 gene were detected. M476I and P574L had been confirmed to be associated with artemisinin resistance. As the withdrawal of chloroquine, the mutant prevalence of Pfcrt and Pfmdr1 genes associated with artemisinin-compatible drug resistance gradually decreased. The resistance of P. falciparum to sulfadoxine-pyrimethamine were mostly “partial resistance”, with no “super-resistant” haplotype detected.