Foeniculum sanguineum Triano & A. Pujadas, sp. nov., from the south western Mediterranean Region (Spain & Morocco) is described. Its characterization and a comparative study with the related species Foeniculum vulgare Mill., has been carried out through morphological, cytological, chemical and molecular analysis. F. sanguineum is distinguished primarily for its red petals, pink pollen in fresh, and red stylopod. It is a diploid species (2n= 22). A high proportion of limonene and piperitenone oxide (absent in F. vulgare) has been found in the essential oil composition of the dry fruits of F. sanguineum and a high amount (about 50 %) of α-phellandrene in its roots and stems. Phylogenetic analyses were performed using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) and the chloroplast rbcL gene sequences. ITS analysis supports the existence of the new species, while revealing sequence divergence both at the intraspecific and at the interspecific levels. A Single-nucleotide-polymorphism (SNP) sequence divergence found in the slow evolving chloroplast gene provided additional support for the novel species characterization, for which the name Foeniculum sanguineum is proposed.