This study compared student scientific reasoning and conceptual knowledge in argumentation-based and traditional instruction, taught in school regions with low and high socio-economic status (SES) respectively. Furthermore, concrete and formal reasoning students' scientific reasoning and conceptual knowledge were compared during both instructions for the examination of science learning equity between student groups. The study sample constituted 26 8th grade students from two schools in a low SES region and 31 8th grade students from a school in a high SES region. The duration of instruction was four months. Students' scientific reasoning and conceptual knowledge were assessed before and after each instruction. According to the results, students who received argumentation-based instruction developed their scientific reasoning following instruction, but students who received traditional instruction did not. In addition, the conceptual knowledge and scientific reasoning gaps between formal and concrete reasoning students, who received argumentation-based instruction, closed, whereas pre-instructional gaps among formal and concrete reasoning students still existed at the end of traditional instruction. Implications from the findings were discussed.