The order Zeiformes comprises a small order of predominantly deep‐sea fishes. However, little information is available on their morphology, such as squamation. Therefore, in the present study, we analysed and described the squamation pattern and scale morphology of five species of Zeiformes occurring on the Brazilian coast: Allocyttus verrucosus, Grammicolepis brachiusculus, Xenolepidichthys dalgleishi, Zenion hololepis and Zenopsis conchifer. Our analysis revealed greater morphological diversity than previously reported for this order. All species, except the scaleless Zenopsis conchifer, presented cycloid scales of spinoid subtype. Grammicolepis and Zenion presented exclusively scales of the spinoid subtype, whereas both Allocyttus and Xenolepidichthys also displayed true cycloid subtype. A. verrucosus is characterised by two distinct groups of scales of different sizes that form scale clusters. G. brachiusculus and X. dalgleishi presented a unique vertically elongated scale covering most of the body. Small bony plates were observed at the dorsal‐ and anal‐fin bases of G. brachiusculus, X. dalgleishi and Z. hololepis. The variation observed is putatively useful for the systematics of the order.