This study was conducted to explore the effectiveness of conceptual change oriented instruction over traditional instruction on students' understanding of acids and bases concept. Besides, effects of gender difference and science process skills on students' understanding of acids and bases were also investigated. Analysis of the results showed that establishing an analogical thinking during the instruction via conceptual change text caused better acquisition of scientific conceptions and elimination of misconceptions. In-depth interviews after the post-tests showed that students' lack of knowledge and misinterpretation of solutions and bonds concepts result in serious misconceptions in acids and bases concept. Especially, students have problems when they relate the concentration and strength with acidity, basicity and pH. Results also showed that science process skills of the students could be a strong predictor of their achievements in acids and bases whereas there was no significant effect of gender on students' understanding of acids and bases.