In this study we investigate students' ability to discern conceptual variation and the use of multiple models in genetics when reading content-specific excerpts from biology textbooks. Using the history and philosophy of science as our reference, we were able to develop a research instrument allowing students themselves to investigate the occurrence of multiple models and conceptual variation in Swedish upper secondary textbooks. Two excerpts using different models of gene function were selected from authentic textbooks. Students were given the same questionnaire-instrument after reading the two texts, and the results were compared. In this way the students themselves made a classification of the texts which could then be compared with the researchers' classification of the texts. Forty-one upper secondary students aged 18-19 participated in the study. Nine of the students also participated in semi-structured interviews. Students recognized the existence of multiple models in a general way, but had difficulty discerning the different models and the conceptual variation that occurs between them in the texts. Further they did not recognize the occurrence of incommensurability between multiple models. Students had difficulty in transforming their general knowledge of multiple models into an understanding of content specific models of gene function in the textbooks. These findings may have implications for students' understanding of conceptual knowledge because research has established textbooks as one of the most influential aspects in the planning and execution of biology lessons, and teachers commonly assign reading passages to their students without further explanation.