Maternal health during pregnancy has been very critical and important for intergenerational health. According to WHO about half of anemia is believed to be due to iron deficiency anemia. In Ethiopia, the anemia prevalence was reported 22% in pregnant and believed due to IDA. Despite recommendation of iron-folic acid supplementation adherence is still low. The objective of the research was to determine the prevalence of folate and vitamin B-12 deficiency among pregnant and association to anemia during second and third trimester. A cross-sectional hospital-based design was conducted to complete this research. 104 pregnant women were selected based on the current altitude adjusted hemoglobin status after informed consent form is signed from each participant. Serum folates, vitamin B-12 were determined using ECLIA and C-reactive protein by Cobas Integra e411. Serum folate, vitamin B-12 and CRP were defined as deficient below 3 ng/mL, 150 pg/mL and greater than 5 mg/L respectively. Data were coded and analyzed using SPSS 22 version. About half of pregnant women were with formal education. 68.1% of pregnant women were anemic based on cutoff point (Hgb<10.9 g/dL). Study participants deficiencies were observed in 27.9% for folate, 26.9% for vitamin B-12 and 23.1% for CRP based on WHO cut-off point. There is a positive association between folate and hemoglobin, low awareness among elder pregnant but, no association between age and hemoglobin value. There is high prevalence of CRP in comparison to previous studies. Supplementation of vitamin B-12 will be recommended including further research on risk factors including rural residents to strength the finding.