According to the timeline of Tamriel, this game takes place before the plague that killed off the native non-reptilian races of black marsh. Does that mean races such as the Lilmothiit and the Kothringi are going to be wandering the swamps?

What time is that? The game takes place somewhere in the middle of the Second Era, and if I had to guess it'd be at this time:

2E 431
Civil wars and insurrection dissolve the Tamrielic Empire.

-6th Century-

2E 533

The events of the Elder Scrolls MMO take place.

2E 560

Knahaten Flu begins, initiated at Stormhold.
Knahaten Flu spreads quickly to the Black Marsh, harshly affecting the population there.

I was guessing 2E 431, the year Potentate Savirien-Chorak and all the heirs of Potentate Versidue-Shaie were assassinated by the Morag Tong, which begins the Interregnum. Otherwise, any time in the Interregnum would be a good fit. Nothing confirmed though.

I'm just going by the Timeline on the Elderscrolls Wiki

533, or (I thought I calculated 532) is give or take a few years roughly 1000 years prior to Skyrim, which is the term bandied about. So that's a pretty good guess. I would give or take a couple hundred years for wiggle room until we hear confirmation.

So to answer your question.... uh... maybe?