Fire corals of the hydrocoral genus Millepora provide an important ecological role as framework 18 builders of coral reefs in the Indo-Pacific and the Atlantic. Recent works have demonstrated the incongruence between 19 molecular data and the traditional taxonomy of Millepora spp. based on overall skeleton growth form and pores. In an 20 attempt to establish a reliable and standardized approach for defining species boundaries in Millepora, we focused on 21 those from the Red Sea. In this region, three species are currently recognized the fan-shaped branching M. dichotoma, 22 the blade-like M. platyphylla, and the massive/encrusting M. exaesa. A total of 412 colonies were collected from six 23 localities. Two mitochondrial marker genes (COI and 16S rDNA) were sequenced to obtain phylogeny reconstructions 24 and haplotype networks. Eight morphological traits of pores and the nematocysts of both polyp and eumedusoid stages 25 were measured to determine if significant morphological differences occur among the three species. Both markers 26 clearly resolved M. dichotoma, M. platyphylla, and M. exaesa as distinct, monophyletic lineages in the Red Sea. 27 Nevertheless, they also revealed deep genetic breaks with Southwestern Indian Ocean populations of the three species. 28 Manuscript Click here to access/download;Manuscript;CORE Arrigoni et al Millepora.docx Click here to view linked References In the Red Sea, the three species were further distinguished based on their pore and nematocyst features. A 29 discriminant analyses revealed dactylopore density, number of dactylopores per gastropore, dactylopore distance, and 30 gastropore diameter as the most informative discriminative characters. The heteronemes, the large and small stenoteles 31 of polyps, and the distribution of mastigophores of eumedusoids also showed significantly interspecific differences. 32 An integrated morpho-molecular approach proved to be decisive in defining species boundaries of Millepora 33 supported by a combination of pore and nematocyst characters which may be phylogenetically informative. colonial organisms building persistent calcareous skeletons and as such playing an important ecological role as 38 framework builders of coral reefs (Lewis 2006). These hydrocorals are among the most relevant reef builders in 39 shallow-water tropical seas, second only to scleractinians (Lewis 1989; Edmunds 1999; Smith et al. 2014). Millepora 40 occurs in tropical and subtropical coral reefs of both the Atlantic and the Indo-Pacific and its depth distribution is 41 restricted from less than 1 m to about 50 m deep because of the obligate symbiosis with zooxanthellae of the genus 42