Microcotyle nemadactylus was first described and redescribed by Dillon & Hargis. Caballero y Caballero and Bravo-Hollis erected the genus Paramicrocotyle to describe Paramicrocotyle tampicensis and Paramicrocotyle atriobursata off Mexico; they placed within this genus 16 species previously assigned to the genus Microcotyle including nemadactylus. However, Microcotyle nemadactylus was returned to the genus Microcotyle and Paramicrocotyle is considered a junior subjective synonym of Microcotyle.
Microcotyle nemadactylus has the general morphology of all species of Microcotyle, with a flat elongated fusiform body comprising an anterior part which contains most organs and a posterior part called the haptor. The haptor is symmetrical and weakly delineated from body proper, bears 94–102 clamps similar in shape and dissimilar in size, arranged as two rows, one on each side. The clamps of the haptor attach the animal to the gill of the fish. There are also two small buccal suckers located at the anterior extremity, and with a rim armed with small, sclerotized, toothlike papillae. The digestive organs include an anterior, terminal mouth, a fairly short esophagus, extending to the posterior margin of the genital atrium, a muscular pharynx, and a posterior intestine with two lateral blind-ending branches. Each adult contains male and female reproductive organs. The reproductive organs include an anterior genital atrium consisting of an outer muscular rim of radiating fibers and an inner portion armed with numerous spines, with spines, a dorsal vagina, a single tubular folded ovary, and 16–25 follicular testes which are posterior to the ovary. The eggs are fusiform, with filaments at both end.