Anatomy faculties are integral to basic science instruction in medical schools, particularly given the preponderance of anatomic instruction in the preclinical curriculum. Recent years have witnessed major curricular restructuring and other emerging national trends that pose significant challenges to anatomists. An examination of anatomy faculty perceptions at two philosophically distinct medical schools within this shifting climate provides an indicator of how different institutional characteristics may impact anatomy instruction and other faculty responsibilities. Semistructured interviews of anatomy faculty from a large, well-established allopathic medical school (Indiana University School of Medicine) and a small, new osteopathic medical school (Marian University College of Osteopathic Medicine) were explored using qualitative thematic analysis. Four overarching themes were identified: (1) Institutional philosophies, such as affiliation with osteopathic versus allopathic medicine, have minimal impact on how the anatomical sciences are taught. (2) Differences in anatomy faculty experiences at these two institutions are largely driven by the institution's size and history. There is a disparity between institutions in the relative importance of teaching and research, but an ability to do research is important for both faculties. (3) Anatomy instruction and research agendas are driven by personal philosophies and interests rather than institutional philosophy. (4) Autonomy is highly valued by anatomists at both institutions. All the participants share a devotion to educating future physicians. In fact, this study identified more similarities than differences in these two faculties. Finally, we argue that shared educational resources and research collaborations can improve anatomy education and faculty development at both institutions.