Graphing is an important practice for scientists and in K-16 science curricula. Graphs can be constructed using an array of software packages as well as by hand, with pen-and-paper. However, we have an incomplete understanding of how students' graphing practice vary by graphing environment; differences could affect how best to teach and assess graphing. Here we explore the role of two graphing environments in students' graphing practice. We studied 43 undergraduate biology students' graphing practice using either pen-and-paper (PP) (n = 21 students) or a digital graphing tool GraphSmarts (GS) (n = 22 students). Participants' graphs and verbal justifications were analyzed to identify features such as the variables plotted, number of graphs created, raw data versus summarized data plotted, and graph types (e.g., scatter plot, line graph, or bar graph) as well as participants' reasoning for their graphing choices. Several aspects of participant graphs were similar regardless of graphing environment, including plotting raw vs. summarized data, graph type, and overall graph quality, while GS participants were more likely to plot the most relevant variables. In GS, participants could easily make more graphs than in PP and this may have helped some participants show latent features of their graphing practice. Those students using PP tended to focus more on ease of constructing the graph than GS. This study illuminates how the different characteristics of the graphing environment have implications for instruction and interpretation of assessments of student graphing practices.