The goal of this study is to map the current state of research in the field of metacognition in science education, to identify key trends, and to discern areas and questions for future research. We conducted a systematic analysis of 178 studies published in peer-reviewed journals in the years 2000-2012 and indexed in the ERIC database. The findings from this analysis indicate that the field of metacognition in science education is in a state of growth and expansion, and that metacognition is increasingly integrated into research addressing the core objectives of science education. In contrast to the findings of previous reviews, conceptual understanding of science was found to be one of the central aims of current metacognition research. The studies employ a wide range of instructional practices for fostering learners' metacognition. The most prominent practice is the use of metacognitive cues and prompts in the course of instruction. Several research gaps are identified: first, the development of learners' metacognitive knowledge is receiving less empirical attention than the development of their metacognitive skills; second, there is a lack of studies that employ controlled research designs that can provide causal evidence regarding the effectiveness of metacognitive instruction for science learning; third, there is an insufficient number of studies of metacognition among young learners in preschool and the early years of elementary school; and fourth, there are very few studies of teachers' knowledge and professional development regarding metacognition. The implications of these research gaps are explored and suggestions for future research are raised.