Aims: This study investigated the effectiveness of cooperative learning strategies on Nigerian Junior Secondary students’ academic achievement in basic science. Study Design: Quasi experimental pretest – posttest – delayed posttest control group design was used by the researchers to carry out the study. Place and Duration of Study: CSIT department, faculty of education, Olabisi Onabanjo University, Ago-Iwoye and Basic science department, school of science, tai Solarin College of Education, Omu-Ijebu, South-west, Nigeria, between March 2009 and October 2010. Methodology: The treatments were at two levels: cooperative learning strategies (learning together and jigsaw II) and conventional lecture method, which was the control group. The moderating variable was anxiety (high and low). Total number of one hundred and twenty students (120) obtained from the intact classes of the three selected Junior Secondary Schools in South-west Nigeria participated in the study. Achievement Test for Basic Science Students (ATBSS), and Basic Science Anxiety Scale (BSAS) were the main Research Article British Journal of Education, Society & Behavioural Science, 2(3): 307-325, 2012 308 instruments used to collect data from students. Descriptive statistics and Analysis of Covariance (ANCOVA) were used to analyze the data collected. Also Multiple Classification Analysis (MCA) was used to determine the magnitude of the mean achievement scores of students exposed to the different treatment conditions. Results: The results of this study indicated that there were significant main effects of treatment on all the dependent measures. There were also significant main effects of anxiety on the students’ post and delayed-post academic achievement scores in basic science. Furthermore, there were significant interaction effects of treatment and anxiety on the academic achievement of students at the posttest and delayed-posttest levels. Conclusion: This study revealed that students in the two cooperative learning strategy (Learning Together and Jigsaw II) groups had higher immediate and delayed academic achievement mean scores than the students in the conventional-lecture group. Learning together and Jigsaw II cooperative teaching strategies were found to be more effective in enhancing students’ academic achievement and retention in basic science more than the conventional-lecture. When friendliness is established, students are motivated to learn and are more confident to ask questions from one another for better understanding of the tasks being learnt.