Abstract There are 43 species of deep-sea eels of 8 families, which including 1 species of Chlopsidae, 2 species of Muraenidae, 3 species of Ophichthide, 14 species of Congridae, 2 species of Muraenesocidae, 2 species of Nemichthyidae, 2 species of Nettastomidae, and 15 species of Synaphobranchidae, which its depth from 150 to 1200 meters and distribution from NE coast to the coast of Taitong and SW coast in Taiwan waters. Meanwhile, there are 3 new species (i.e., Dysomma longirostrum, Ophichthus aphotistos, Synaphobranchus sinensis) and 11 new records (i.e., Chilorhinchus platyrhynchus, Ophisurus macrorhynchus, Rhechias retrotincta, Macroceohenchelys brachialis, M. soela, Japonoconger sivicolus, nettastoma solitarium, Meadia abyssale, Dysommina rugosa, Ilyophis brunneus, Synaphobranchus kaupi) are described. The study in this part also recognize vertebral formulae is useful of elucidating the difference among the species. Morphology of swimbladder, stomatch, gonads of the deep-sea eels and the melanin layer of diaphragm are able to be as a distinctive character to find out the relationship among the species and the families. Most eels¡¦ reproductive season concentrate on September to November, whatever, the synaphobranchids have two reproductive seasons, which are on May and September to October. And it should become important to make further research on the above phenomenon. True eels (anguilliforms) form a monophyletic taxon from 16 apomorphic characters, e.g., Well-developed olfactory bulbs, lateral-protruded telencephalon, large-sized tectum, a distinct gap between telencephalon and tectum, reduced neural arch, hamel arch, and uroneural, triangled urostyle, epural absent, convergent hypural, fused hypural 1-2 and hypural 3-4-5, gap between hypural 1-2 and parhypural, and a gap between hypural 1-2 and hypural 3-4-5. The present study also find (1) Muraenoidei and angulloidei are a sister ¡Vgroup by sharing a slit between telencephalon and tectum, smaller olfactory bulb and lobe, and slit on area posttrema; (2)Congroidei is a monophyletic group by sharing an oval tectum, large cerebellum, and ungrooved area postrema, fusion of hypural 3, 4, and 5; (3) Congroidea and Synaphobranchoidea share a fusion of parhypural with hypural 1 and a concave present between uroneural and hypural, which should be treated as a sister group; (4) most eels of Congridae share a FS-caudal-fin and should be treated as a clade; (5) Most eels of Ophichthidae share a reduced and degraded caudal-fin, which should be monoplyletic; (6) Synaphobranchinae¡BSimenchelyinae and Ilyophinae, uniquely sharing well¡Vdeveloped olfactory bulb, small telencephalon, lateral protrusion of telencephalon well developed, and cerebellum folded posteriorly, a CLC- caudal-fin and elevated hypural 3-4-5, and fusion of hypural 4 and 5, are belong to a monophyletic group; (7) a gap between parhypural and hypural 1 indicate Simenchelyinae and Ilyophinae should be treated as a sister group; (8) Eurypharynx, Cyema, and Monognathus sharing a reduced caudal fin and brain, which need further research to elucidate their relationship; (9) Dark-red saccus vasculosus appears to recommend a close relationship between Gavialiceps taeniola and duckbill eels. (10) A disc-like hypophysis suggests the eels, Albula, Pterothrissus, Notacanthus, Megalops, and Elops are closely related groups; (11) Albula, Pterothrissus, Megalops, and Elops share a distinct morphological type of tectum and cerebellum and they should be treated as closely related groups; (12) The brains¡¦ gross morphology of Albula, Pterothrissus, Megalops, and Elops are well developed, a correlation distinctly similar to that of the Clupea which need further study on the relationship among the taxa mentioned above and the Clupeiformes.