BackgroundFatty acid desaturases(FADs) are involved in regulating plant fatty acid composition by adding double bonds to growing hydrocarbon chain. Apart from regulating fatty acid compositionFADsare of great importance, and are involved in stress responsiveness, plant development, and defense mechanisms.FADshave been extensively studied in crop plants, and are broadly classed into soluble and non-soluble fatty acids. However,FADshave not yet been characterized inBrassica carinataand its progenitors.ResultsHere we have performed comparative genome-wide identification ofFADsand have identified 131 soluble and 28 non-solubleFADsin allotetraploidB. carinataand its diploid parents. Most soluble FAD proteins are predicted to be resided in endomembrane system, whereas FAB proteins were found to be localized in chloroplast. Phylogenetic analysis classed the soluble and non-soluble FAD proteins into seven and four clusters, respectively. Positive type of selection seemed to be dominant in bothFADssuggesting the impact of evolution on these gene families. Upstream regions of bothFADswere enriched in stress relatedcis-regulatory elements and among them ABRE type of elements were in abundance. Comparative transcriptomic data analysis output highlighted thatFADsexpression reduced gradually in mature seed and embryonic tissues. Moreover, under heat stress during seed and embryo development seven genes remained up-regulated regardless of external stress. ThreeFADswere only induced under elevated temperature whereas five genes were upregulated underXanthomonas campestrisstress suggesting their involvement in abiotic and biotic stress response.ConclusionsThe current study provides insights into the evolution ofFADsand their role inB. carinataunder stress conditions. Moreover, the functional characterization of stress-related genes would exploit their utilization in future breeding programs ofB.carinata and its progenitors.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04232-9.