This research provided quantitative and qualitative evidence of beginning science teachers\u27 knowledge and implementation of four of the science education teaching standards (Standards A, B, C and D) as described in the NSES (1996) using data from portfolios produced by teachers as a requirement for licensure in Connecticut. The study was comprised of three phases. Phase one involved a large-scale exploration of the performance of all teachers who produced portfolios during the 2001–2002 academic years (N = 368). The distribution of performances across four levels of performance (unsatisfactory, basic, proficient and advanced) are quantitatively described for the entire portfolio (a holistic measure of standards based performance), on four tasks within the portfolio (lesson design, implementation, assessment, reflection), and, finally, of teachers\u27 performances on 14 performance indicators aligned with the NSES. In phase two, eight genetics portfolios were qualitatively analyzed to explore teachers\u27 knowledge of standards based on the theoretical construct of pedagogical content knowledge (PCK). Five components of PCK were analyzed: knowledge of content; students\u27 learning needs; assessment; topic-specific instructional strategies; and orientation toward science teaching. In phase three, the teachers\u27 five factors related to their teachers\u27 pre-service preparation (knowledge of biology, type of pre-service preparation, and teachers\u27 knowledge, training and assessment on standards) were statistically analyzed as predictors of teachers\u27 implementation of standards. ^ Results indicated that beginning science teachers were most challenged by the following aspects of the NSES teaching standards: Standard A, addressing students\u27 learning needs; Standard B, implementation of science inquiry; and Standard C, assessment of students\u27 learning of science concepts and processes. ^ Analysis of PCK indicated that most teachers did not demonstrate the guided inquiry orientation toward science teaching in their unit design but were able to incorporate some inquiry processes in their daily teaching. Teachers\u27 topic specific PCK for teaching genetics indicated that teachers were not proficient in using models to support the learning of genetics concepts and did not have sufficient knowledge of how to implement strategies for teaching socioscientific issues related to genetics. The five pre-service factors were not predictors of teachers\u27 success in the implementation of the NSES teaching standards measured through the portfolio assessment.