The use of phylogenetic tools and studies has strongly increased in the last two decades especially in conservation biology and community ecology. Phylogenetic trees are essential to understand the processes of community or network assembly, to identify centers of diversification, and to help protect Earth’s evolutionary heritage. Despite two decades of research and syntheses, there are still many discussions on how phylogenetic diversity (PD) methods should be effectively applied to those fields. In particular, conservation approaches based on PD have become similar to these used in community ecology. Thus, the main benefit of using PD calculations in conservation biology may have been ignored or misinterpreted. Our goal is to discuss and provide guidelines to the use of PD in biodiversity conservation so that its benefits are not hidden or lost in the approaches employed. We also aim that benefits and uses are better recognized and more easily understood by researchers or practitioners who would like to include PD in their studies and conservation planning.