In the present study Scilla luciliae, S. forbesii, S. sardensis, S. siehei, Scilla x allenii and S. bifolia are compared anatomically. Some differences have been found in root, scape, and leaf anatomy of the taxa, and commented. S. luciliae, S. forbesii, S. sardensis and S. siehei have a metaxylem at the center of the root, others have 3-4 number metaxylem. Vascular bundles in two row in S. luciliae and S. forbesii in a single row in S. sardensis, Scilla x allenii and S. bifolia though in three rows in S. siehei. Aerenchyma tissue is present in mesophyll of five taxa leaf except S. sardensis. The anatomical variations in the taxa have been investigated by means of numerical methods (Analysis of variance and Pearson correlation). By the analysis of the investigated taxa from 12 anatomy related characters, it has been also found that the results from numerical analysis of anatomy characters can provide additional evidences, which correspond to the anatomy for the recognition of the taxa.