This study aimed at identifying the effect of teaching physics using metacognitive thinking skills in physics concepts achievement and in developing scientific thinking skills amongst physics students in light of their gender as compared to using conventional methods. To achieve the study purposes, two instruments were used: one for physics concepts achievement; the other for scientific thinking skills. The instruments were applied on the sample of the study, which consisted of 64 second year physics students at Al al-Bayt University during the scholastic year 2010/2011. The sample was randomly assigned into two groups: the experimental group (30 male and females students) was taught the “Waves& Vibration” course by using metacognitive thinking skills whereas the control group (34male and female students) was taught the course by the conventional method. The quasi-experiment study lasted for four months. The findings of the study revealed that teaching physics using metacognitve thinking skills was more effective than the conventional teaching method in improving students\' achievement in physics concepts and in enhancing their scientific significant difference thinking skills. The results also indicates no statistical significance due to the interaction between the teaching method and gender. According to these results, some recommendations were offered.