Distinguishing features of L. brachyphyllum include its stem hyalodermis, costa usually with a single layer of ventral stereids, small upper leaf cells with simple to bifid papillae scattered over the cell lumina, and short, non-porose inner basal leaf cells. Leptodontium filicola is similar to L. brachyphyllum in most of these features but it is a smaller plant (3 vs 6 cm high) with stiffly incurved to falcate-incurved, oblong-lanceolate leaves, broadly acute to obtuse leaf apices, and propagula clustered at the stem apex. Although Zander (1972) figured propagula for L. brachyphyllum  he did not describe them in either of his treatments of the species (1972, 1994). All Central American material of L. brachyphyllum examined lacked propagula. Leptodontium pungens differs from L. brachyphyllum in having 2–4 layers of ventral stereids in its costa and smooth, linear, often porose inner basal leaf cells. Leptodontium brachyphyllum is similar to L. capituligerum in having somewhat differentiated outer/inner basal leaf cells, and both species have unistratose, quadrate-celled enations from basal leaf cells at their leaf insertions. Leptodontium capituligerum differs from L. brachyphyllum in having smooth inner basal leaf cells that are very strongly differentiated from the outer basal cells, and complex, coroniform leaf cell papillae. Leptodontium longicaule is also somewhat similar to L. brachyphyllum but it is a more robust species with complex, coroniform papillae centered over the lumina of the upper leaf cells.