Eleocharis tenuis belongs to the E. tenuis complex, which comprises species 16–21 and is restricted to North America, where it is widely distributed except for the Southeast and Southwest. Eleocharis occulta, E. bifida, and E. nitida are very distinct, have little variation, and have relatively restricted ranges; E. tenuis, E. elliptica, and E. compressa are difficult to separate, are highly variable, and have relatively large ranges (see also discussions under E. compressa and E. elliptica). Eleocharis occulta and E. bifida are evidently closely related to E. compressa; they are known only from unglaciated areas south of the limits of Pleistocene glaciation, while E. compressa has a broad range in glaciated regions. The cytotaxonomic study by L. J. Harms (1972) of E. tenuis, E. elliptica, and E. compressa included artificial interspecific and infraspecific hybrids as discussed under those species.
Eleocharis tenuis var. pseudoptera might also be treated as E. elliptica var. pseudoptera following L. J. Harms (1972) because it is intermediate between E. tenuis var. tenuis and E. elliptica var. elliptica in most characters except for the 4-angled, usually deeply sulcate culms. It appears to intergrade with E. elliptica. It is placed in E. tenuis because many plants, including an isotype, are more like E. tenuis than E. elliptica; because most plants key more easily to E. tenuis; and to continue the use of the traditional name. The achenes of the holotype (from Lancaster county, Pennsylvania) and some other specimens closely resemble those of E. elliptica but are not obviously persistent after the scales fall. The usually diagnostic tooth on the distal leaf sheath in E. tenuis var. pseudoptera is also characteristic of E. elliptica var. elliptica; but in E. tenuis var. pseudoptera it is more often present and usually longer and stouter than in E. elliptica. The culms of the holotype of E. tenuis var. pseudoptera and many other specimens are 4- to 5-angled, and in some specimens are very irregularly to 6-angled and often rigid and compressed. L. J. Harms (1972) transferred E. tenuis var. pseudoptera to E. elliptica because he counted the same 2n = 38 chromosome number in both E. elliptica and E. tenuis var. pseudoptera and produced artificial E. elliptica × E. tenuis var. pseudoptera hybrids in which meiotic pairing and pollen stainability were very high. A. E. Schuyler (1977) reported 2n = 39 for E. tenuis var. pseudoptera as well as 2n = 34 and 68 for a putative E. tenuis var. tenuis × E. tenuis var. pseudoptera hybrid.
Putative hybrids between Eleocharis compressa and E. erythropoda of the E. palustris complex in Ontario have been reported (P. M. Catling and S. G. Hay 1993), and I have observed putative E. compressa × E. erythropoda and E. elliptica × E. erythropoda hybrids in the field in southeastern Wisconsin. It seems possible that introgression from E. erythropoda is responsible for some of the variation of both E. compressa and E. elliptica, especially the frequent presence of some 2-fid styles and lenticular achenes in both species and some (rarely all) entire floral scales in E. compressa (S. G. Smith 2001).