Eye degeneration is a general evolutionary tendency shown in many animal groups that are adapted to dark environments. Thus far, the degenerative process has only been discussed within a few taxonomic units, in terms of both evolution and development, and more studies are needed to deal adequately with this area of ostracod biology. The ostracods and copepods examined in the present study are small crustaceans that are widely diversified in the aquatic environment, and also in interstitial environments, and their 'nauplius eyes' (primitive eye in Crustacea; typically composed of three or four ocelli) show various degrees of degeneration. The ultrastructure and ontogeny of their degenerated nauplius eyes are described for the first time in the present study, using transmission electron microscopy. According to our observations, two morphotypes for degenerative nauplius eyes (i.e. 'tapetal-less form' and 'pigment reduced form') are found in both taxa. The first description of the embryogenesis of normal (none-degenerated) nauplius eyes of surface species is also provided. From a comparison between the embryogenesis of normal nauplius eyes and the postembryogenic development of the 'tapetal-less form', it is strongly suggested that the 'tapetal-less form' is derived by paedomorphic evolution. On the basis of our observations, as well as on previous studies, we propose the hypothesis that modularity, in the form of hierarchical interactions, exists in the nauplius eye (i.e. the tapetal cells constitute an independent developmental module to be distinguished from other developmental or functional modules, including both the pigmented cells and the sensory cells). According to our hypothesis on the nauplius eyes, we also discuss the possibility that the degenerative process is constrained within the general developmental and functional context.