The new species Ecsenius springeri is described from 6 specimens, 32.7–42.8 mm SL, collected at the Kokas area of the Fakfak Peninsula in the Bird’s Head Seascape of western New Guinea, West Papua Province, Indonesia. The new species is a member of the Bicolor Group of Ecsenius, which also contains E. bicolor and E. namiyei. The group is distinguished from congeners in having cirri on both the anterior and posterior rims of the anterior naris (vs. on the posterior rim only) and in commonly having multiple vertical pairs of pores in the lateral line. Ecsenius springeri is most closely related to E. bicolor and superficially resembles the striped variety of that species. However, it consistently differs in having a narrower black mid-lateral stripe that ends more anteriorly; a more distinct white stripe along the mid-side of the body; a more extensive orange area on the posterior half of the body; and either lacks a pinkish-to-orange diagonal band behind the eye or, if present, it is very faint. The two species diverge by 8.5% in the mtDNA COI barcode marker sequence (mean K2P).