Dichotomous keys provide a systematic approach to classification and identification but have been minimally explored as a teaching tool in medical histology education. Active learning strategies have been shown to improve engagement and retention, yet structured identification tools remain underutilized. This study aimed to evaluate whether peer-led dichotomous key sessions improve confidence, knowledge, short-term retention, and practical examination performance among osteopathic medical students. Two 60-minute peer-teaching sessions were conducted with voluntary first-year DO students enrolled in musculoskeletal and gastrointestinal histology courses. A pre-session survey assessed eligibility and excluded students repeating the course or enrolled in a master’s program. Baseline confidence was measured at four time points using self-reported Likert scales. Pre-quizzes assessed baseline knowledge and confidence. Sessions included brief instruction on dichotomous key construction, followed by individual practice and team-based application using premade keys. Post-quizzes assessed knowledge and confidence after instruction, and a post-survey following the practical reassessed confidence. Practical exam scores of participants (n = 32–36) were compared with nonparticipants (n ≈ 145) using independent-samples t-tests. Participants achieved an average musculoskeletal practical score of 86% compared with 83% among nonparticipants (p = 0.089). In the gastrointestinal session, participants scored 89.5% compared with 85.9% (p = 0.046). Quiz scores improved by 34%. Qualitative feedback indicated increased confidence, engagement, and recognition of histologic features. Limitations include self-selection bias, single-institution design, and a smaller intervention group. Peer-led dichotomous key instruction may offer a low-cost, structured strategy to enhance early histology learning and student confidence.