Zygodon is a genus of erect, sparsely branched plants with mostly lanceolate to linear-lanceolate leaves, having uniform, isodiametric upper leaf cells, terminal perichaetia, cucullate calyptrae, long setae, and cylindrical, deeply furrowed capsules. The combination of erect stems and cucullate calyptrae separates the genus from most other Central American Orthotrichaceae. The type of the genus is European, but most of the species are tropical; Lewinsky (1989a) considered Andean South America (with 49 of 90 species) to be its center of diversity. Significant variation within the genus is found in its leaf margins (entire or dentate), leaf cell ornamentation (papillose or smooth), basal leaf cell shape (linear and thick-walled or rectangular, enlarged and thin-walled), leaf apex (acute or obtuse), and especially in its peristome (double, single and  endostomial with 8 or 16 segments, or absent). Goffinet & Vitt (1998) re-established the genus Codonoblepharon, and segregated those species previously treated in Zygodon sect. Obtusifolii as Bryomaltaea. The former is based upon plants with leaves having smooth cells and enlarged, thin-walled, basal cells. Section Obtusifolii is based solely on plants with obtuse leaf apices. These weak segregates of Zygodon are best treated at the subgeneric level.

When sporophytes of Zygodon are absent, the genus can be confused with Anoectangium and Leptodontium in the Pottiaceae (see Zander & Vitt 1979) or Amphidium (Dicranaceae). Anoectangium differs from Zygodon in having a stem central strand, and large, bifid to multiplex papillae. In addition, it never has the type of propagula often found in Zygodon. Leptodontium differs from Zygodon in having larger, more crowded, usually multiplex papillae (often O‑ or C‑shaped), and strongly recurved basal leaf margins. Leptodontium flexifolium is often confused with Zygodon because the two are similar in size. In addition to the above noted distinctions, that species differs from Zygodon in having more strongly toothed leaf margins that are often lighter in color, forming an indistinct border. Amphidium differs from Zygodon in having long, linear leaves that are strongly crisped and contorted when dry, leaf cell papillae that extend over the lumina and adjacent cell walls as longitudinal striae, and immersed to shortly exserted capsules.

The genus was revised by Malta (1926). Lewinsky (1989a) more recently revised the Australasian members of Zygodon.