New networking technologies increase the effectiveness and the adoption of interactive tools in all education levels. Concept maps are one of the most important of these interactive tools. They have been widely used as learning and teaching tools in science education. The purpose of this study is to investigate the effectiveness of web-supported concept maps (WSCMs) and classical concept maps (CCMs) on students' cognitive development and misconception changes about photosynthesis subject. The sample of this study consists of total 74 students and 2 experienced teachers in Trabzon. CCMs were transferred to the virtual environments in the form of WSCMs by authors. At the beginning, Photosynthesis achievement tests (PAT) and photosynthesis concept test (PCT) were administered as pre-tests and post-tests both to experimental group and control group. After the educational program, general science achievement on PAT increased by 10 % in favor of experimental group (EG) at significant level (p<0.05). Although the increased at knowledge level in cognitive development was 16.00 % in the EG and 16.80 % in control group (CG). These changes were 26.60 % and 18.90 % at comprehension and application levels in the EG and 10.54 %15.50 % in the CG for cognitive development, respectively. The results revealed that using WSCMs in teaching photosynthesis is very effective for students to reach comprehension level of cognitive domain. In addition, misconceptions about food, nutrition and energy sources for plants were decreased in the EG more than in the CG.