Malaria is a protozoal disease caused by Plasmodium spp parasite transmitted by an infected female mosquito as it bites the human host. It is one of the most common causes of infectious disease related deaths in the World with Africa bearing the largest proportion of the world's malaria burden because the region hosts the anopheles mosquito which is the most efficient malaria vectors, and also due to lack of the basic infrastructure and resources necessary for efficient and sustainable control of the malaria disease. Despite the wide control strategies, occurrence of malaria is on the increase with an estimated incidence rate of 37% globally and 42% in Africa. In Uganda, malaria is the leading cause of morbidity and mortality and is responsible for 40% of all outpatient visits, 25% of all hospital admission and 14%of all hospital deaths. The study objective was to determine the prevalence of malaria and associated control methods among pregnant women attending focused antenatal care at Iganga Main Hospital, Iganga District. A descriptive cross sectional study was conducted in June 2017 at Antenatal Care Clinic, Iganga Main Hospital, and Iganga District, Uganda. Quantitative data was collected by means of questionnaires covering a study population of 126 pregnant mothers where a systematic random sampling method was used. 52/126 (41.3%) were found positive to malaria parasites and majority of pregnant women were aged 20-30 years, these had highest infection rate of 44.2% (38/86),with primigravidas having the highest infection rate of 54.8%. It was also observed that according to gestational age of pregnancy, women of first trimester had the highest prevalence of 68.3% (28/41). The study showed that the most common barrier method used to prevent malaria was treated mosquito nets with 76/126 (60.3%). In general, pregnant mothers had fair knowledge about malaria control methods. Despite focused antenatal care and the awareness on malaria control methods, a malaria prevalence of 41.3% was scored. Therefore interventions aimed at social and behaviour change are necessary to address the gaps highlighted by the study. Keywords: Malaria, mosquito, Plasmodium, mosquito nets