Recent molecular analyses have challenged the traditional classification of scleractinian corals at almost all taxonomic levels, suggesting a requirement of new morphological characters for classification. Microskeletal characters have shown great potential to support the classification of the molecular-based clades of the scleractinian corals. Flabellum (Family Flabellidae) is the fifth largest genus and contains two subgenera, F. (Flabellum) and F. (Ulocyathus). The genus is very important in deciphering flabellid evolution, as phylogenetic relationship is still ambiguous in this family. In particular, little is known of the microstructural features of Flabellum species. Here we discuss the microskeletal structures of F. (F.) magnificum and F. (U.) deludens. Rapid accretion deposits (RADs) on the walls of F. (F.) magnificum show dome-shaped strands ca. 50–100 µm wide, which are composed alternatively of microcrystalline and fibrous parts. In contrast, the RADs on the walls of F. (U.) deludens consist of strands (50–100 µm long and 20–30 µm wide) made up of very short fibers (ca. 0.5–5 µm long) or microcrystallines with meniscus structure and dome-shaped fibrous layers. Thickening deposits (TDs) on the walls of both species are characterized by three qualities: (1) layered bundles consisting of fibrous crystals; (2) shingle-like TDs composed of small crystals and microcrystallines; and (3) shingle-like TDs comprised of larger fibers. In particular, in F. (U.) deludens, the TD of the calicular side of the wall is mainly formed of shingle-like TDs. The walls of F. (U.) deludens and F. (F.) magnificum thus differ completely in terms of the RAD (digitated strand and dome-shaped fibrous layers vs. continuous dome-shaped alternation) and TD characteristics. These kinds of microskeletal differences could support the molecular phylogenetic distinction between the F. (U.) spp. cluster and the F. (F.) clusters.