The classification and generic definition in the tropical–subtropical fern family Lindsaeaceae have been uncertain and have so far been based on morphological characters only. We have now studied the evolutionary history of the Lindsaeaceae by simultaneously optimizing 55 morphological characters, two plastid genes ( rpoC1 and rps4) and three non-coding plastid intergenic spacers ( trnL-F, rps4-trnS and trnH-psbA). Our data set included all genera associated with Lindsaeaceae, except Xyropteris, and c. 73% of the currently accepted species. The phylogenetic relationships of the lindsaeoid ferns with two enigmatic genera that have recently been included in the Lindsaeaceae, Cystodium and Lonchitis, remain ambiguous. Within the monophyletic lindsaeoids, we found six well-supported and diagnostic clades that can be recognized as genera: Sphenomeris, Odontosoria, Osmolindsaea, Nesolindsaea, Tapeinidium and Lindsaea. Sphenomeris was shown to be monotypic; most taxa formerly placed in that genus belong to the Odontosoria clade. Ormoloma is embedded within Lindsaea and therefore does not merit recognition as a genus. Tapeinidium is sister to a clade with some species formerly placed in Lindsaea that are morphologically distinct from that genus and are transferred to Osmolindsaea and Nesolindsaea, proposed here as two new genera. We do not maintain the current subgeneric classification of Lindsaea itself, because neither of the two generally accepted subgenera ( Lindsaea and Odontoloma) is monophyletic, and most of the sections also appear unnatural. Nesolindsaea shows an ancient biogeographical link between Sri Lanka and the Seychelles and many of the main clades within Lindsaea have geographically disjunct distributions. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163, 305–359. [ABSTRACT FROM AUTHOR]