BackgroundHistone modification is an important epigenetic regulatory mechanism and essential for stress adaptation in plants. However, systematic analysis of histone modification genes (HMs) in Brassicaceae species is lacking, and their roles in response to abiotic stress have not yet been identified.ResultsIn this study, we identified 102AtHMs, 280BnaHMs, 251BcHMs, 251BjHMs, 144BnHMs, 155BoHMs, 137BrHMs, 122CrHMs, and 356CsHMsin nine Brassicaceae species, respectively. Their chromosomal locations, protein/gene structures, phylogenetic trees, and syntenies were determined. Specific domains were identified in several BrassicaceaeHMs, indicating an association with diverse functions. Syntenic analysis showed that the expansion of BrassicaceaeHMsmay be due to segmental and whole-genome duplications. Nine keyBnaHMsin allotetraploid rapeseed may be responsible for ammonium, salt, boron, cadmium, nitrate, and potassium stress based on co-expression network analysis. According to weighted gene co-expression network analysis (WGCNA), 12BnaHMswere associated with stress adaptation. Among the above genes,BnaPRMT11simultaneously responded to four different stresses based on differential expression analysis, whileBnaSDG46,BnaHDT10, andBnaHDA1participated in five stresses.BnaSDG46was also involved in four different stresses based on WGCNA, whileBnaSDG10andBnaJMJ58were differentially expressed in response to six different stresses. In summary, six candidate genes for stress resistance (BnaPRMT11,BnaSDG46,BnaSDG10,BnaJMJ58,BnaHDT10, andBnaHDA1) were identified.ConclusionsTaken together, these findings help clarify the biological roles of BrassicaceaeHMs. The identified candidate genes provide an important reference for the potential development of stress-tolerant oilseed plants.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04256-1.