Contrary to the situation at primary, middle, and secondary school levels, university science courses provide students with very few opportunities to reflect upon the nature of science (NOS). The first goal of this study was to provide evidence that the co-construction of evolutionary trees, an important component of university biology education, can be used as a platform to introduce undergraduates to some aspects of NOS, such as the importance of (1) hypothesis, (2) human creativity, and (3) cooperation and collaboration in the development of scientific knowledge. The second goal was to provide evidence that this approach could be used without sacrificing student mastery of the drawing of phylogenetic trees in a scientific and reasonable way. The data was derived from 68 undergraduates’ (39 females and 29 males, 17–22 years old) written responses and audio and video recordings in a university biology course in Colombia. The findings show that the co-construction of phylogenetic trees can offer potential contributions to the introduction of undergraduates to some aspects of NOS and the promotion of their understanding of these visual representations. This study contributes to the development of a research-based university science education that can inform the design of a NOS curriculum for higher education.