Introduction: Malariais caused by parasites of the Plasmodium family and transmitted by femaleAnopheles mosquitoes.About 3.2 billion people were at risk of the disease in the world, and an estimated 198 million cases occurred in the year 2016.Malariaaffects over 60% of the 94 million total population of Ethiopia.Plasmodium falciparum accounts for nearly 70% of all malaria cases while the remaining are due to P. vivax. Methodology: A facility based cross-sectional study was conducted in Doyogena district from July 2016-June 2017. One primary hospital and three health centers were included purposely from facilities of Doyogena district.Study participants were selected by their population proportion from those facilities which included in the study and every febrile case was interviewed until the sample size reached. Data were collected by a pre-tested structured questionnaire and were entered to Epi-Info software version 3.5.4 and exported to SPSS version 16 for descriptive and logistic regression analysis. Sample size was calculated using single population formula using Stat Calc Epi Info Version 7 and equals to be 293 and adding 10% none response rate finally 487 study subjects. Data would be entered to Epi Info version7 and analyzed by SPSS version 20. Interviewer structured questionnaire would be used to collect data. Results: A total of 487 participants were involved in the study making the response rate of 100%. The mean age was 25.86 years [ranging: from 1 year to 80 years] and SD was ±15.620 years. Also females accounts 279 (57.3%) and males accounts 208 (42.7%).Overall slide positivity in the study area was 2.67% with (34.8%) plasmodium falciparum and (65.2 %) cases were plasmodium vivax species. Bed net use[AOR: 6.857, 95%CI: (1.783, 26.369)], travelling to malaria endemic areas [AOR: 5.406, 95% CI: (3.292, 35.23)] and presence of surface water around home [AOR: 0.146, 95% CI: (0.35, 0.611)] were significantlyassociated factors with malaria when adjusted for all other variables Conclusion: This study showed that malaria is still a health problem also in a low transmission areas and P. vivax was the dominant Plasmodium species in the study area among febrile cases.Low proportion of ITNs distribution and absence of Insecticide Residual spray activities was observed in the study areas. Not using bed net, travel history to endemic areas and residing near stagnant surface water were factors with associated malaria positivity in the study area.