This study addresses the gender differences of cognitive processes involved in program debugging. In the experiment, twenty-five participants were asked to find bugs in the test programs. Eye-movement analysis was employed to track the students' gaze paths while they traced and tried to debug the programs. Cognitive processes were then obtained by employing sequential analysis of gaze data to investigate the significant sequences of attention areas. Cognitive processes of different genders were investigated by comparing the tracing sequences of program debugging. The experimental results show that both genders had limited working memory capacities for debugging the iterative program with complex computation. But females needed more manual calculation for the recursive program in this study. For the iterative structure, females tended to grasp the program requirements and then trace into the major part of the program, while males traced the change of output value according to the logic of the iterative statements. For the recursive problem, females traced the flow of recursive induction and the stop condition to execute the program and find bugs, while males traced the recursive function in a more leaping way. This study leaks the gender differences of cognitive processes in program debugging, based on which instructors/researchers can develop adaptive computer programming instruction for students of different genders.