Our knowledge of species diversity in deep-sea chemosynthetic communities has come a long way since their discovery in the late 1970s, However, their study poses serious challenges that are linked to their remoteness, the variable selectivity and effectiveness of sampling tools in different conditions, a lack of consensus on the size compartments and sieve size used in practice, and the persistent discovery of species that are previously unknown to science. Still, with increasing accessibility and new sampling tools, quantitative data are becoming both more frequent and extensive, reducing limitations in the estimation and comparison of species diversity. Here, we review the literature for common difficulties encountered in the measurement and comparison of species diversity within and among deep-sea chemosynthetic communities. We lay out recommendations for future and ongoing work that should lead to more accurate evaluations and more robust comparisons. We advocate: (1) complete transparency in the taxonomic levels used to compute reported diversity measures and public access to data tables after publication; (2) an effort to standardize size compartments and sieves used within the research community; (3) the use of families of species diversity measures that allow for differential weighting of abundant and rare species; (4) the evaluation of the completeness of inventories and the stability of all diversity measures for all groups of samples under comparison; and (5) caution in the use and interpretation of statistical tests on species diversity. Only through appropriate tools can we hope to gain the knowledge and understanding necessary for the management and protection of the often endemic fauna found in deep-sea chemosynthetic communities.