Organizational design implementations frequently fail, with existing dominant frameworks and tools, such as the ever-present maturity assessments, falling short in addressing the complex, nonlinear nature of socio-technical systems (STS). This paper introduces PhylOrg, a methodology leveraging phylogenetic analysis to guide organizational design by mapping evolutionary pathways of socio-technical traits (STTs). By identifying coherent and efficient sequences of change, PhylOrg minimizes resistance and aligns initiatives with organizational contexts. Grounded in theories of complex adaptive systems (CAS) and evolutionary processes, PhylOrg proposes to offer prescriptive, context-sensitive guidance to Organizational design leaders. A pilot study demonstrates PhylOrg’s potential, highlighting foundational evolutionary traits as prerequisites for more advanced capabilities.