Malaria remains a major public health challenge in Nigeria, particularly among vulnerable groups such as pregnant women. This study assessed the prevalence of malaria infection among individuals with different haemoglobin genotypes attending antenatal care at Zainab Bulkachuwa Hospital, Gombe. A retrospective cross-sectional design was adopted, involving the analysis of 180 antenatal records with complete genotype and malaria test data. Results revealed a high overall malaria prevalence of 63.9%, indicating endemic transmission. The HbAA genotype was the most prevalent (61.1%) and exhibited the highest malaria infection rate (72.7%), followed by HbAS (54.5%) and HbSS (33.3%). Variations were also observed in parasite density, with HbAA individuals showing higher levels of parasitaemia compared to other genotypes. Statistical analysis using Chi-square demonstrated a significant association between haemoglobin genotype and malaria infection (p = 0.004). The findings confirm that haemoglobin genotype influences susceptibility to malaria, with HbAS and HbSS offering some protective advantage. The study underscores the need for targeted malaria control strategies and the integration of genotype screening in antenatal care to improve maternal health outcomes.