This study aimed to determine the prevalence of bacterial vaginosis (BV) and aerobic vaginitis (AV) and their associated risk factors among pregnant women from Ethiopia. Also, this study investigated the bacterial pathogens and their antibiotic resistance in AV cases. A total of 422 pregnant women from northern Ethiopia were participated in this study. Socio-demographic and clinical data were recorded. Vaginal swabs were collected and used for wet mount and Gram stain methods to evaluate the AV and BV scores according to the Nugent's and Donder's criteria, respectively. In AV cases the bacterial pathogens and their antibiotic resistance were determined using standard methods. The possible risk factors for AV and BV in pregnant women were investigated. The prevalence rates of BV and AV were 20.1% (85/422) and 8.1% (34/422), respectively. BV was more common in symptomatic vs. asymptomatic people (P < 0.001), and in second trimester vs. first trimester samples (P = 0.042). However, AV was more common in secondary school vs. primary and those who were unable to read and write (P = 0.021) and in housewife women vs. employee (P = 0.013). A total of 44 bacterial strains were isolated from AV cases, of which the coagulase-negative staphylococci (CoNS) (38.6%) and Staphylococcus aureus (29.5%) were the most predominant bacteria, respectively. The highest resistance rate was observed against penicillin (100.0%) in staphylococci, while 86.7% of them were sensitive to ciprofloxacin. The resistance rate of Enterobacteriaceae ranged from 0.0% for ciprofloxacin and chloramphenicol to 100.0% against amoxicillin/clavulanate. The prevalence of BV was higher than AV in pregnant women. This higher prevalence of BV suggests that measures should be taken to reduce the undesired consequences related to BV in the pregnancy. The circulation of drug-resistant bacteria in vaginal infections requires a global surveillance to reduce the risks to pregnant mothers and infants.