This study aims to analyse the difference of metacognitive awareness of treatment (using Blended Project Based Learning) and control class. This is a quasi-experimental research with Non-equivalent Control Group Design. This research was conducted at Department of Biology Education, University of Muhammadiyah Malang, in the first semester of the academic year 2014/2015. Metacognitive awareness of treatment class and control class was measured by using Metacognitive Awareness Inventory. Metacognitive awareness difference analysed with One-way ANOVA, processed with SPSS 22 for Windows. The results showed that there were difference Mean values in metacognitive awareness (knowledge about cognition and regulation of cognitive) between treatment and control. Mean value of treatment class was higher than control class. It means that Blended Project Based Learning effectively to develop and stimulation metacognitive awareness of new students (Biology teachers candidates).