Sodium-dependent cation chloride cotransporters (NaCCC) participate in transepithelial salt movement. AeNKCC1 is the Aedes aegypti ortholog to Ncc69, a Drosophila melanogaster electroneutral Na-K-2Cl cotransporter. In contrast, aeCCC2 and aeCCC3 may be electrogenic and potassium-independent, despite their sequence similarity with aeNKCC1. We hypothesize that these functional differences reflect differences in primary amino acid sequence of the transmembrane domains (TMD). We developed R code to explore amino acid conservation across TMDs of the NaCCCs from 10 mosquito species. Within each paralog, the TMDs are more than 90% conserved across species (NKCC1: 95% +/- 6, CCC2: 91% +/-9, CCC3: 92% +/- 5.7, n = 10). Across paralogs, the TMDs are less well conserved with average conservation ranging between 62 and 95%. Conservation varies by TMD. The conservation of TMDs 1, 6, and 10 is between 83% and 95%; the conservation of TMDs 2, 3, 4, and 8 is between 70% and 77% and the conservation of TMDs 5, 7, and 9 is between 61% and 70%. Across all 10 TMDs, 66% of residues are fully conserved both within NKCC1 and within CCC2 paralogs; of those residues, 35% differ between the paralogs. Similarly, 64% of residues are fully conserved both within NKCC1 and within CCC3; 32% differ between paralogs. Although 57% of residues are fully conserved within both CCC2 and CCC3, only 6% of those residues differ between the paralogs. Across all ten TMDs, less than 0.5% of residues were fully conserved within each paralog but had a different amino acid in each paralog. Thus, conservation between CCC2 and CCC3 is higher than conservation between either paralog and NKCC1. The fully conserved residues that differ between the NKCC1 and CCC2/CCC3 paralogs are good candidates to explore for roles in the functional differences between the paralogs.