In addition to being parasites themselves, copepods are subject to parasitic infection. The most common parasites are marine dinoflagellates of the genus Blastodinium, which are gut parasites of many copepod species. Twelve species of Blastodinium are described, the majority of which were discovered in the Mediterranean Sea. Most Blastodinium species infect several different hosts, but species-specific infection of copepods does occur. Generally, adult copepod females and juveniles are infected.
During the naupliar stage, the copepod host ingests the unicellular dinospore of the parasite. The dinospore is not digested and continues to grow inside the intestinal lumen of the copepod. Eventually, the parasite divides into a multicellular arrangement called a trophont. This trophont is considered parasitic, contains thousands of cells, and can be several hundred micrometers in length. The trophont is greenish to brownish in color as a result of well-defined chloroplasts. At maturity, the trophont ruptures and Blastodinium spp. are released from the copepod anus as free dinospore cells. Not much is known about the dinospore stage of Blastodinium and its ability to persist outside of the copepod host in relatively high abundances.
The copepod Calanus finmarchicus, which dominates the northeastern Atlantic coast, has been shown to be greatly infected by this parasite. A 2014 study in this region found up to 58% of collected C. finmarchicus females to be infected. In this study, Blastodinium-infected females had no measurable feeding rate over a 24-hour period. This is compared to uninfected females which, on average, ate 2.93 × 10 cells per day. Blastodinium-infected females of  C. finmarchicus exhibited characteristic signs of starvation, including decreased respiration, fecundity, and fecal pellet production. Though photosynthetic, Blastodinium spp. procure most of their energy from organic material in the copepod gut, thus contributing to host starvation. Underdeveloped or disintegrated ovaries and decreased fecal pellet size are a direct result of starvation in female copepods. Parasitic infection by Blastodinium spp. could have serious ramifications on the success of copepod species and the function of entire marine ecosystems. Blastodinium parasitism is not lethal, but has negative impacts on copepod physiology, which in turn may alter marine biogeochemical cycles.
Freshwater copepods of the Cyclops genus are the intermediate host of the Guinea worm (Dracunculus medinensis), the nematode that causes dracunculiasis disease in humans. This disease may be close to being eradicated through efforts by the U.S. Centers for Disease Control and Prevention and the World Health Organization.