What one considers desirable ways of teaching and learning science is influenced by one's conception of science. Therefore, what constitutes good science teaching can be better understood by understanding what the teacher's conception is. Teachers' perception of students and how they learn science is also influenced by how they teach science. The present study is based on a case study of two science teachers (a male and female), whose perceptions about how boys and girls learn science and practices in a coeducation classroom have been explored. The study sought to answer two questions: What are science teachers' (a female and a male) perceptions about how girls and boys learn science in secondary schools in Pakistan? How do these perceptions influence their teaching practices in science classes? Data was collected mainly through interviewing and observing the classrooms of a male and a female science teacher, teaching a coeducation class. The findings of this study indicate that science teachers have many unexamined perceptions that influence their practices. The findings of these perceptions indicate that teachers think that science requires experiments and asking questions. They also think that science (with the exception of biology) is for boys. The practices' findings tend to marginalize or exclude girls from learning science in co-education classes in Pakistan. They have higher expectations from boys than from girls, they call on boys more often than girls to answer questions and use examples more common to boys' experiences. This is because the teachers' knowledge of science and pedagogy is limited. Furthermore, there is a clear evidence that teachers' perceptions and practices in co-education classes favor boys. It also indicates that there is a gap between teachers' perception and teaching of science. Although the purpose of the study is not to give suggestions for the renovation of perceptions and practices of the teachers in science classroom, implications are drawn for teachers and teacher educators which may assist in making science classroom more fair gender-wise.