The short-beaked echidna (Tachyglossus aculeatus) is 1 of 5 extant species of monotreme, found only in Australia and Papua New Guinea. The aim of this study was to identify the species of coccidia present and establish a range of subclinical Eimeria spp. (Coccidia: Apicomplexa) oocyst shedding in echidnas from eastern Australia over 18 mo. The coccidia were detected in 89% (49/55) of fecal samples from 12 long-term monitored and healthy captive echidnas, 75% (3/4) of 4 healthy long-term captive echidnas, 83% (5/6) of 6 short-term captive echidnas, and 60% (6/10) of 10 wild echidnas. Echidnas captive for 4 to 23 yr shed 100–46,000 oocysts g−1 of E. echidnae and remained clinically healthy during this study. Sub-adult and adult wild, and short-term captive, echidnas shed oocysts of both E. echidnae and E. tachyglossi. The lack of coccidia in juvenile short-beaked echidnas suggests these animals are probably non-immune and should not be placed in environments heavily contaminated with oocysts. In addition, no oocysts were found in captive long-beaked echidnas (Zaglossus bartoni bartoni, n = 2) housed at Taronga Zoo. This study represents an important step in understanding the host–parasite interaction between coccidia and short-beaked echidnas.