Abstract: Wood anatomy is one of the tools used for taxonomic classification of species. By combining this tool with molecular phylogeny, the current groupings made in morphological studies can be discussed. This study describes the wood anatomy of the monotypic genera of Cupressaceae and analyses the features that could represent synapomorphies of the principal clades recovered by molecular phylogeny. The wood anatomical study shows the high homogeneity of this family, revealing the presence of common ancestral features that support the union between Taxodiaceae and Cupressaceae s.s. and the separation of Sciadopitys. It also supports the group formed by Taxodiaceae in Cupressaceae s.l. No clear division was observed between the callitroid and cupressoid clades. Some wood anatomical differences were observed in the Fitzroya–Diselma–Pilgerodendron and Microbiota–Platycladus Tetraclinis associations. The wood anatomical features common to the family, such as axial tracheids without helical thickenings, homogeneous rays, cupressoid cross-field pits and the presence of a warty layer, are put forward as possible synapomorphies for Cupressaceae s.l. The clade-specific synapomorphies are taxodioid cross-field pits for taxodioid and sequoioid clades, absence of a well-defined torus in Thuja–Thujopsis and torus extensions in Diselma–Fitzroya–Widdringtonia.