The prevalence of endoparasites associated with chaetognath abundance in the coastal waters of the Mexican Central Pacific was studied fortnightly from November 2010 to December 2011. A total of 35 (0.21%) out of 16,407 chaetognaths were found to be parasitized. Five out of twelve chaetognath species (Flaccisagitta enflata, F. hexaptera, Parasagitta euneritica, Serratosagitta pacifica, Zonosagitta bedoti) were found to be parasitized by nine endoparasitic taxa: Protists (two morphotypes), digenean metacercariae [Didymozoidae, Hemiuridae, Parahemiurus sp., Lepocreadiidae, Prosorhynchus sp. (Bucephalidae)], and cestodes (metacestodes) [Tetraphyllidea (two morphotypes)]. Parasagitta. euneritica and Z. bedoti were the most abundant chaetognath species, and Protist sp. 2 and Tetraphyllidea sp. 1 were the most abundant parasites. The highest prevalence for most of the endoparasite species occurred in June, and the values varied according to three hydroclimatic periods: stratified (S), semi-mixed (SM), and mixed (M). Eight non-infected chaetognath species, two parasitized chaetognaths (F. enflata and S. pacifica), and two parasites (Protist sp. 1 and Tetraphyllidea sp. 2) were associated with warm temperatures (S and SM periods); in contrast, P. euneritica, Z. bedoti, parasitized F. hexaptera, and the parasite Tetraphyllidea sp. 1 showed a strong local preference for cooler temperatures, high productivity, and high biomass conditions (M periods). We discovered the occurrence of the digenean Prosorhynchus sp. (Bucephalidae) parasitizing the chaetognath P. euneritica, and this is the first report of Prosorhynchus parasitizing chaetognaths worldwide. We also confirmed the presence of Lepocrediidae (metacercariae larval stage) infecting F. hexaptera, a parasite that had only been recorded infecting other chaetognaths of the Atlantic Ocean. The parasite diversity affecting the chaetognath populations of the Central Mexican Pacific coast likely differs between the offshore, outer slope areas, and the surveyed coastal system.