The structure of hitherto-unknown exocrine glands in the caudal rami of the pelagic copepods of the genus Calanus was investigated, together with the vertical, diel and seasonal variations in the occurrence of granules secreted from the glands. Zooplankton samples were collected in Sagami Bay by vertical tows of a net from 4 discrete layers at 250-m intervals in the upper 1000 m both day and night, with an additional seasonal sampling in the upper 200 m. The samples contained copepodids of Calanus sinicus (stages IV–VI), C. jashnovi (stages IV–V), and unidentified Calanus (stages I–III), which possessed the glands regardless of the developmental stage and sex. Each caudal ramus has an inner- and an outer gland each of which opens in a pore at the ventral base of a caudal seta. According to light microscopy the cavities of only the inner glands contained many transparent granules, some of which appeared to have been discharged to the environment. The granules were present regardless of day/night, depth, and season, with the maximum number of 52/copepod. The cells surrounding the inner cavity contained well-developed rough endoplasmic reticulum, mitochondria, Golgi-bodies, and secretory granules; the outer cavity contained granules of much lower density than those in the inner cavity. These observations rule out the possible functions of the glands for egg and sex pheromone production, and suggest most likely function is predator avoidance. However, neither has mechanical disturbance excited luminescence, nor has ultraviolet emission excited fluorescence, suggesting the secretion is non-luminescent. Alternative possible functions include secretion of defensive substances or substances that might enhance swarm formation. A survey of preserved copepod collections indicated presence of similar glands in Calanus helgolandicus, C. pacificus, Cosmocalanus darwinii, Mesocalanus tenuicornis, and Nannocalanus minor, suggesting evolution of the glands in the common ancestor of these species that comprise a monophyletic group within the Calanidae.