To improve oral hygiene education, we evaluated the perception and potential impact of microbiology-focused oral hygiene instructions (OHI) given to pregnant patients. Dental hygienists provided this supplemental education and administered Saliva-Check Mutans (SCM) tests to pregnant patients (n = 188) in Obstetrics and Gynecology (OB/GYN) settings. Patients reported their self-perceived understanding of the relationship between oral bacteria and dental disease and returned postdelivery to receive a second SCM test and follow-up questionnaire (n = 47). Prior to the hygienist instruction, 84% of participants understood that bacteria caused tooth decay, while only 36% understood they could transfer these bacteria to their children. After instruction, patient understanding increased to 97% and 95%, respectively. Participants attributed these increases to the hygienist’s explanation and SCM test. In postdelivery participants, >80% reported adherence to routine oral hygiene practices, and a significant decrease in patients with high-risk levels of salivary Streptococcus mutans was determined by SCM test (p = 0.0253). Participants agreed that the SCM test (89%) and microbiology explanation (95%) should be provided to every pregnant patient. Evaluation of patient perception of this intervention highlights how focused instruction on the infectious nature of dental disease can increase perinatal oral health literacy. Microbiology-focused education should be given to pregnant patients to reduce oral health disparities.