When you see these two species, they are easy to tell apart as E. marnockii is at least 2-3 times the size of E. cystignathoides.
Token photos -
E. marnockii - rocky, hill country canyons

E. cystignathoides - usually a suburban backyard frog (but spreading rapidly)

The problem is that I often record vouchers for NAHerp of calling frogs and there have been a few cases where I was in habitat that suggested E. marnockii, but close enough to a residential area to make me suspect E. cystignathoides.
So I set out this summer to record both and figure out the difference. In case you care, here's what I learned.
Both species have two "types" of calls. More complex trill like calls which are easy to tell apart and their single chirp note calls which sound almost the same to me.
So I recorded some known individuals and compared their calls and spectra of those chirps, and here's what I learned.
I cut and pasted a series of chirp calls from different frogs and different localities (and different dates) in the following order. See if you can hear the difference. The order is
marnockii - 6 chirps
cystignathoides - 4 chirps
marnockii - 1 chirp
cystignathoides - 6 chirps
cystignathoidess - 4 chirps
marnockii - 4 chirps (with crickets)
Click this link to hear the call comparison.
The difference is obvious when you hear them together. The question is can I learn to distinguish when I only hear one species?
If you look at the spectra for this recording, you can see the difference. E. marnockii's calls are all right around 2000-2500 khz while E. cystignathoides range from 2500 - 4000 khz.

(In case you care and aren't used to reading spectra, the small vertical bars labeled represent the chirps and the Y axis is the frequency (pitch) in khz. The bars for the E. marnockii calls are lower than the E. cystignathoides calls because the call is lower in pitch. The X axis is time. Play the recording again and watch the spectra, counting the chips as they call.)
I doubt I will ever learn to distinguish whether the call was above or below 2500 khz, but I can always check the spectra if I record it I guess.
Anyway, just thought it was interesting. Another herp ID tool for me at least.
In case anyone cares, all the cut-and-paste recording and the spectrum were produced in the free (and awesome) audio program Audacity.
Chris