Silica frustules of most planktonic diatoms have many shallow holes in which the length (L) is smaller than the width (W). The present study focuses on a silicic ultrastructure of the setae of a planktonic diatom having deep (L/W > 1) holes. Here, we characterized nanoholes on the silica walls of hollow setae of a colony of Chaetoceros coarctatus. Basically, tetragonal poroid arrangements with and without a costa pattern are observed on the inner and outer surfaces, respectively, for three kinds of curving hollow setae. Deep nanoholes ∼90 nm wide are elongated from 150 to 1500 nm (L/W ∼17) with an increase in the wall thickness of the polygonal tubes of the setae. The inside poroid array, with a period of 190 nm in the extension direction of setae, is lined by parallel plates of the costae. However, the poroid arrangement on the outer surface is disordered, with several holes obstructed with increasing wall thickness of the posterior terminal setae. According to the movement of a colony in a fluid microchannel, the thick curving terminal setae is suggested to involve attitude control and mechanical protection. Using an optical simulation, the patterned deep through-holes on the intercalary setae were inferred to contribute anti-reflection of blue light for the promotion of photosynthesis in seawater.