Although there are reports of permineralised woods in Mesozoic and Cenozoic strata in Mexico, there are few palaeobotanical studies based on coniferous stems. Four taxa of fossil wood from three localities in Mexico are described at the anatomical level and identified taxonomically based on detailed comparisons with woods of extant and fossil taxa. Agathoxylon gilii sp. nov. and A. jericonse sp. nov. are determined from the Todos Santos Formation (Upper Jurassic), in Chiapas; A. parrensis sp. nov. is described from the Las Encinas Formation (Palaeocene) in Coahuila; and Taxodioxylon cabullensis sp. nov. corresponds with material from the Packard Shale Formation in Sonora. Dominance of Araucariaceae and Cupressaceae in this region during the Mesozoic and early Cenozoic is further supported by leaf records, but these materials may also represent other taxa, like Cheirolepidaceae, which may have araucarioid secondary xylem. Records of Brachyphyllum and/or Pagiophyllum, which may represent araucarioid or cheirolepidaceous taxa, and different cupressaceous leaves, have been collected in rocks of the same period in nearby formations. At present, the amalgamation of isolated organs to form one plant is uncertain and, thus, there is an open challenge to reconstruct the plants and better understand these extinct communities. The new fossil taxa will add to the diversity of extinct plants and conifer communities during the Mesozoic and early Cenozoic in low-latitude North America.