Oocysts attributable to Eimeria macusaniensisGuerrero et al. 1971, were found in coprolites and in archaeological sediments dating to the Holocene of Patagonia, Argentina. By means of a nonparametric regression using a generalized additive model, a significant relationship was found between the size of the oocysts and their antiquity. Specifically, a reduction in oocyst size over time was discovered, probably due to a parasite response to host replacement, to an extinct eimeriid species common during the Pliestocene-Holocene transition, or to environmental changes known for the Holocene. Explanations regarding coevolution between parasites, hosts, and paleoenvironmental conditions are discussed herein.