The purpose of this study was to collect and analyse data from a class of low achieving students, the focus was on their behaviour and perceptions during a cooperative learning unit of work in science. The data were used to ascertain two things: Are there any gender related differences in behaviour or perceptions of cooperative group learning in science for low achieving students during the unit of work; and what conditions were necessary for females and males to work cooperatively in mixed gender groups in science. Results indicated that when group work was not structured for interdependence, individual accountability and use of positive social skills, negative interpersonal relationships emerged. This resulted from participation patterns of female dominance and male reluctance. When group work was structured for interdependence, individual accountability and use of social skills cooperation occurred between females and males. Schools should consider use of well structured cooperative learning to encourage low achievers, female participation and cooperation between females and males in science classes.