Horsetails (Equisetum, Equisetaceae) are one of the oldest groups of vascular plants with a nearly continuous fossil record dating back to the Carboniferous. Only a few studies have addressed relationships among and within the extant members of this fern genus. We here present the first complete phylogenetic analysis of one or more samples of all extant species covering the full geographical range. Using three plastid loci, we evaluate species limits, taxon circumscription and inter-relationships. Several known hybrids were also included to confirm their parentage. All species for which we included multiple samples are found to form discrete groups, but many infraspecific taxa appear not to warrant recognition. We found strong support for the placement of E. bogotense as sister to the rest of the genus, supporting recognition of a third subgenus in Equisetum, described in this paper as E. subgenus Paramochaete. We have evidence for acceptance of additional species, E. braunii and E. xylochaetum. We accept the American E. praealtum as separate from E. hyemale and we tentatively recognize two varieties in E. ramosissimum. A nomenclatural checklist, including accepted taxa, synonymy and distributions, is provided. Two new combinations are made and 77 names are typified.