One of the goals of college-level introductory biology is to establish a foundation of knowledge and skills that can be built upon throughout a biology curriculum. In a reformed introductory biology course, we used iterative model construction as a pedagogical tool to promote students' understanding about conceptual connections, particularly those linking genetic variation to organismal fitness. In interviews conducted 2.5 years later, we examined students' retrieval of conceptual connections emphasized during the course. Students constructed a model similar to those practiced during the course, reviewed their models with the interviewer, and answered questions about how they retrieved this knowledge conceptual understanding. Student proficiency on this task was evaluated based on the quality of their modeling and responses to questions about their models. Three distinct groups emerged: students that had an inadequate cognitive structure for the biological concepts (absent), and students that had incomplete or complete cognitive structures. Students in the Complete group were better able to verbally link genetic variation to phenotypic variation and differential fitness and successfully used relationships stored in their cognitive structure to explain gaps present in their drawn model. Students in the Incomplete group had fragmented knowledge where some concepts were connected to each other, but not to the whole model. Students in the Absent group had extensive gaps in knowledge and were unable to connect their conceptual ideas. Students who were most proficient in the task differed in their ability to access and search within their cognitive structure and verify the quality of their conceptual relationships. This allowed the most proficient students to fill in knowledge gaps and transfer their conceptual understanding to new contexts.