In order to compete in a global economy, students are going to need resources and curricula focusing on critical thinking and reasoning in science. Despite awareness for the need for complex reasoning, American students perform poorly relative to peers on international standardized tests measuring complex thinking in science. Research focusing on learning progressions is one effort to provide more coherent science curricular sequences and assessments that can be focused on complex thinking about focal science topics. This article describes an empirically driven, five-step process to develop a 3-year learning progression focusing on complex thinking about biodiversity. Our efforts resulted in empirical results and work products including: (1) a revised definition of learning progressions, (2) empirically driven, 3-year progressions for complex thinking about biodiversity, (3) an application of statistical approaches for the analysis of learning progression products, (4) Hierarchical Linear Modeling results demonstrating significant student achievement on complex thinking about biodiversity, and (5) Growth Model results demonstrating strengths and weaknesses of the first version of our curricular units. The empirical studies present information to inform both curriculum and assessment development. For curriculum development, the role of learning progressions as templates for the development of organized sequences of curricular units focused on complex science is discussed. For assessment development, learning progression-guided assessments provide a greater range and amount of information that can more reliably discriminate between students of differing abilities than a contrasting standardized assessment measure that was also focused on biodiversity content.