Fagaceae in northern Thailand consists mainly of three genera : Castanopsis, Lithocarpus and Quercus, eash with extensive species diversity. A selected study area of about 550 km² called Pa Khun Mae Kuong at Doi Saket district in Chiang Mai province including two different types of habitats: hill evergreen forests at relatively high elevation (1000-1800 m) and deciduous forests at altitudes below 800 m. Samples were collected from 146 trees: leaves, fruits (acorns) and flowers for taxonomic identification; young leaves for DNA extraction; and leaf buds for chromosome isolation, although occasionally flower buds and root tips were also used. Based on the morphological characters, 30 species were identified from this collection, consisting of 12 Castanopsis, 11 Quercus and 7 Lithocarpus species. Castanopsis was dominant in Hill evergreen forests, whereas Quercus occurred mainly in Deciduous forests. Lithocarpus was found in all forest types. The genetic relationship among these species was analysed using data on restriction fragment length polymorphism (RFLP) in the 18S-25S ribosomal genes (rDNA) and inter-simple sequence repeats (ISSR). The results included (1) clear separation of the genera and of most species, supporting the taxonomic classification, (2) Castanopsis being genetically diverse, Quercus relatively homogeneous, but Lithocarpus showing a split diversity, and (3) strong indication of gene flow between Castanopsis and Lithocarpus, and between Lithocarpus and Quercus, which may have been the reason behind the diversity pattern of Lithocarpus in this region. The species and genetic diversity was also analysed using chromosome and genome data, from karyotypes and fluorescence in situ hybridization (FISH) mapping of the 18S-25S and 5S ribosomal genes on chromosomes. Most species were found to be diploid (2n = 24), with relatively conserved karyotypes and ribosomal gene maps within each genus. Nevertheless, aneuploidy and polyploidy samples were detected and the FISH analysis indicated hybridity in some samples. The cytogenetic results confirmed the molecular and taxonomic diversity of this plant group.