How is the relation between the Thalmor and Black Marsh?

Rather distant. The Thalmor do see Argonians as lesser as they do men and so will, one day, aim to kill or enslave the Saxheel. But men are the biggest threat to the elves due to their (relatively) rapid birth rate. read more

The Argonians control all of Black Marsh, the Southern Half of Morrowind and are possibly the most stable of the Provinces. They have no immediate enemies and are growing in power. The Nords, Imperials, Bretons and Redguards are weakened and are constantly fighting the Thalmor. The Dumner have been all but destroyed. read more

Remember, the Thalmor aren't actually opposed to the Stormcloak rebellion. Although the White-Gold Concordat was technically a truce between the Thalmor and the Empire, it was really just the Empire surrendering to the Thalmor under duress. The Thalmor do not trust the Empire, nor does the Empire trust the Thalmor. read more

While it is true that Black Marsh has never in its history seen that kind of unified national order, it's also important to note that Black Marsh has never operated as it has recently before. It's behaviour in the recent decades of the 4th era is completely out of character - they have almost never acted as a single force before or seen themselves as one nation. read more