http://www.reefmonitor.org/documents...rinol.%202.pdf
They do an assessment of cortisol and corticosterone levels from fecal matter, and find that baseline levels of aquarium acclimatized fish and reef dwelling parrotfish are not statistically different.
As for the testing of fecal matter vs direct (blood) measurement, they do both to validate the former method, and find that pooling fecal matter is an acceptable and useful metric for assessing stress hormone levels.