Is there human DNA in fecal matter?

Because faecal matter contains sloughed-off gut cells, there will be some DNA mixed in. However, because it will also contain dead bacteria and other biological molecules, and because the digestive enzymes could have damaged the DNA, it will most likely be too contaminated with foreign DNA and too degraded for research.

Yes, there is DNA from shed epithelial cells and mitochondrial DNA can be found in well preserved coprolites.

Coprolites were used to provide new evidence for when N. American natives were resident in Oregon. Eske Willerslev has worked on extracting DNA from extinct, frozen mammals and gained good results. He took coprolites from the Paisley Caves excavation run by University of Oregon archaeologist Dennis Jenkins. Some proved to be human.

"The results, Jenkins says, were "earth-shaking." Both labs agreed that the coprolites were left 14,300 years ago--almost 1,500 years before the earliest agreed-upon evidence for human presence in the Americas. "For the first time, we are actually radio-carbon dating human remains that are pre-Clovis," Jenkins says. "There are older radiocarbon dates on sites in North America, but not directly on human remains."

http://www.archaeology.org/online/features/coproli...

DNA testing is more accurate if you have a specific suspect.

However, part of the fecal material is cells shed from the lining of your gut. It might be a bit trickier than other samples (relatively low concentration of your own cells vs. other material and microbes), but it can be done.

according to an article in ScienceDaily