The Santolina chamaecyparissus complex includes 13 species of dwarf aromatic evergreen shrubs from the western Mediterranean Basin. Five native species occurring in Italy are currently accepted. Four of them are endemic to relatively restricted areas in the peninsula, whereas S. corsica Jord. & Fourr. is endemic to Corsica and Sardinia. The taxonomic treatments of Italian Santolina have been changing significantly in the past, probably due to the misinterpretation of naturalised populations of S. chamaecyparissus, a widely cultivated pentaploid species, which occasionally escapes from cultivation through agamospermy or vegetative propagation. In this study, we carried out the first quantitative morphometric and comparative niche analyses concerning the four species endemic to continental Italy (S. etrusca, S. ligustica, S. neapolitana, and S. pinnata). Morphometric analyses (PCoA, Random Forest, and univariate analyses) show that these species can be easily distinguished by combinations of character states, whereas niche analyses (Schoener’s D and similarity test) suggest that they occur in distinct climatic conditions. Based on our results, we fully confirm the taxonomic distinctiveness of these species. An updated identification key, including all Santolina species occurring in Italy, is presented.