Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process by solving a problem in the context of authentic research in genetics. Through the learning environment, the learners are exposed to a genetics problem which was developed on the basis of research in which a mutated gene, which causes deafness, was identified. They follow, step by step, the way scientists try to solve it, using the current geneticists' toolbox. The environment uses an adapted version of the BLAST program (a bioinformatics tool which enables to find similarities between sequences), which was modified in a way that enables the teachers and students to use it easily. Using quantitative and qualitative research approaches, we were able to show that learning through the bioinformatics environment promotes construction of new knowledge structures and influences students' acquisition of a deeper and multidimensional understanding of the genetics domain. In addition, learning through the bioinformatics environment influences students' comprehension of the practices and scientific ways of thinking. (Contains 1 table and 1 figure.)