Micropaleontology is a critical tool for determining the ages of geologic records, reconstructing ancient environments, and monitoring modern ecosystem health. However, most students are not exposed to micropaleontology in their college coursework. To enable non-expert instructors to integrate microfossil identification training in their undergraduate courses, we developed FossilSketch, an interactive web-based educational tool that introduces students to the basics of micropaleontology and guides students through a scaffolded learning experience that develops microfossil identification skills. Here we test the impact of FossilSketch on students' ability to learn micropaleontology skills, such as identification of microfossils to genus level and basics of fossil data analysis, using data on students' performance and survey responses collected in an undergraduate paleontology course for geology majors at a large public university. A total of 112 students took part in this study. Analysis of classroom assessments showed that junior and senior geology majors who used FossilSketch were better able to understand the process of microfossil identification, recognize morphological characteristics, and achieve a correct identification than those who did not use FossilSketch. Students who used FossilSketch needed to ask the teaching assistant fewer questions and felt better prepared for specimen-based work than students who did not use FossilSketch. These results suggest that FossilSketch improves students' understanding of the microfossil identification process.