Introduction: Malaria is a deadly disease that puts approximately 3.3 billion people at risk globally. Migrants traveling to endemic area are high risk groups that are mostly affected by malaria. Dangure woreda is a low land area located at altitude below 2000 meter and stratified under high risk for malaria. No previous study done in the study area. Therefore, this study aimed at assessing the prevalence of malaria and associated factors among migrant and indigenous residents of Dangur woreda, Benishangul Gumuz Region, West Ethiopia, 2020. Methods and Materials: community-based comparative cross-sectional study design was conducted in dangur woreda from November to December 2019. Simple random sampling technique was used to select the study participants. Pre-tested structured questionnaires used for data collection. Rapid Diagnostic Test was used to determine the prevalence of malaria. Data entry and analysis was done by EPI Info-7 and SPSS-20respectively. Binary logistic regression was used to determine the association between dependent and independent variables. All variables with p-value< 0.2 by bivariate analysis were entered to multivariable analysis. Finally statistically significant association was declared at 95% CI and p-value of <0.05. Results: The overall malaria prevalence was 15.3 % (95% CI= 12.3-18.0). The prevalence among indigenous was 11.5 % (95% CI = 8.2-14.8) and migrants was 19.3 % (95% CI = 14.9-24). The difference in malaria prevalence between the two population was -7.8 % (95% CI = -13.5 to -2.0) which is statistically significant at p-value of 0.008. In combined multi-variable analysis, family size of ≥6 (AOR=2.3, 95% CI=1.4-3.7), having no insecticide treated net (AOR=6.9, 95% CI=3.3-14.5), age group between 15-24 (AOR=6.9, 95% CI=2.4-21.0), age group 25-34 (AOR=4.0, 95% CI=1.4-12.1), age group 35-44 (AOR=3.7, 95% CI=1.2-11.6) and wood/bamboo house wall (AOR=2.6, 95% CI=1.6-4.5) were a risk factors for malaria. Insecticide treated net utilization (AOR= 0.37, 95% CI=0.21-0.67) and being male in sex (AOR=0.50, 95% CI = 0.31-0.82) were found to reduce the odds of malaria infection. Conclusion & recommendations: The overall prevalence of malaria was high. Malaria prevalence was high among migrants than indigenous residents. age, female gender, family size >6, not having TN, and material of wood/bamboo house wall were risk factors. Malaria intervention programs should be strengthened and addresses migrant labourers. Keywords; malaria prevalence, risk factor, indigenous, migrants, Ethiopia