Provided that they are unsporulated (as opposed to already sporulated) in a fresh fecal specimen, then they might well be oocysts of Cystoisospora (= Isospora); in which case it  would be easier to identify them to the generic level morphologically than by using molecular techniques. Place a fecal sample in a SHALLOW layer of, ideally, 2.5% potassium dichromate (failing which water) in a covered Petri dish. Keep it on the laboratory bench, i.e. at room temperature. Lift the cover about 4 times daily for 2 to 3 days and each time agitate the contents of the dish for a minute or two with a pipette. Thereafter, do a flotation. If the (now) sporulated oocysts are seen to contain 2 sporocysts (each with 4 sporozoites in them), and the size of the oocysts is MORE than about 15 microns in diameter, they are probably those of Cystoisospora. If there are e.g. 4 sporocysts (each containing 2 sporozoites) in an oocyst, then that is another story.

Dear Miles,

Thank you very much for your thoughtful input!  Unfortunately, the samples are already fixed in 70% ethanol.   Chao

Thanks, Chao. This explains your question. I have certainly found (long ago) Cystoisospora in African mongooses, including a new species that I did not name. Oocysts in fecal specimens that were fixed sometimes gave away their generic identity because two sporocysts had started to form inside a few of the oocysts before fixation. It is unlikely that, in the present state of knowledge as regards coccidia of mongooses, you would be able to make a species identification on the basis of PCR + sequencing.

I am coming literature and trying to find primers for amplifying a wide spectrum of organisms.  I might have already found them .  Will keep you posted once I have any positive news.  Thank you so much for your invaluable information, Miles!

OK, Chao. Perhaps, if you are lucky, more might be known about intestinal coccidian species that have been recorded from "your" mongoose than is known concerning coccidia in some other mongoose species.