Alyssum kaynakiae is an endemic biennial species growing in Southwest Anatolia, Turkey. In this study, the morphology of this taxon was revised, and its anatomical, palynological, and karyological characteristics were analysed for the first time. Alyssum kaynakiae has been considered part of the traditional Alyssum sect. Gamosepalum. Alyssum kaynakiae has diploid chromosome number 2n=16. It has a primary structure in the root and stem, collenchyma located under the epidermis in the root and under the cortex layer in the stem, and vascular bundles varying between 9 to 11. Leaves are isolateral, stomata are at the same level as the epidermis, and both sides of the leaves have lepidote hairs. Its palynological features are compatible with the Brassicaceae family, with its pollen type being tricolpate, its pollen shape being prolate, and its ornamentation being reticulate.