This study analyzed third-year undergraduate Chemistry major students’ drawings and written explanations of substitution reactions. Seventy (70) students were purposively selected for this study. The main data collection instrument was a diagnostic test, and students’ responses were analyzed using deductive coding. The study aimed to unearth students’ conceptual understanding and difficulties with substitution reactions to provide significant insights into improving teaching strategies and learning outcomes. The findings revealed that: 1. Students were more familiar with SN2 reaction mechanisms and could answer questions on SN2 reaction mechanisms better than SN1 reaction mechanisms;2. Students’ use of ‘chemical vocabulary did not translate into an understanding of electron movement and causal mechanistic explanation; 3. About 97 % of the students who gave a correct/partially correct description provided a description of what was happening in the reaction without any further explanation of why the reaction occurred; 4. Students had a slightly better understanding of drawing the correct mechanisms than of providing accurate explanations. This study recommends that, in teaching organic reaction mechanisms, instructors should emphasize electron-pushing formalisms and explain how and why reactions occur to encourage mechanistic thinking in students. Also, students should be given ample practice in organic reaction mechanisms to improve mastery.