Coagulase-negative staphylococci (CNS) are isolated commonly from bovine milk and skin. Their impact on udder health and milk quality is debated. It has been suggested that sources and consequences of infection may differ between CNS species. Species-specific knowledge of the impact and epidemiology of CNS intramammary infections is necessary to evaluate whether species-specific infection control measures are feasible and economically justified. Accurate measurement of impact, sources, and transmission mechanisms requires accurate species level identification of CNS. Several phenotypic and genotypic methods for identification of CNS species are available. Many methods were developed for use in human medicine, and their ability to identify bovine CNS isolates varies. Typeability and accuracy of typing methods are affected by the distribution of CNS species and strains in different host species, and by the ability of test systems to incorporate information on new CNS species into their experimental design and reference database. Generally, typeability and accuracy of bovine CNS identification are higher for genotypic methods than for phenotypic methods. As reviewed in this paper, DNA sequence-based species identification of CNS is currently the most accurate species identification method available because it has the largest reference database, and because a universally meaningful quantitative measure of homology with known species is determined. Once sources, transmission mechanisms, and impact of different CNS species on cow health, productivity and milk quality have been identified through use of epidemiological data and accurate species identification methods, appropriate methods for routine use in research and diagnostic laboratories can be proposed.