In the second type the principal characters of the Dipnoi are manifest, and some of them, for example Dipterus, Palædaphus, Holodus, approach so closely the Dipnoi which still survive, that the differences existing between them warrant a separation into families only.
Devonian fishes are frequently found under peculiar circumstances, enclosed in the so-called nodules. These bodies are elliptical flattened pebbles, which have resisted the action of water in consequence of their greater hardness, whilst the surrounding rock has been reduced to detritus by that agency. Their greater density is due to the dispersion in their substance of the fat of the animal which decomposed in them. Frequently, on cleaving one of these nodules with the stroke of the hammer, a fish is found embedded in the centre. At certain localities of the Devonian, fossil fishes are so abundant that the whole of the stratum is affected by the decomposing remains emitting a peculiar smell when newly opened, and acquiring a density and durability not possessed by strata without fishes. The flagstones of Caithness are a remarkable instance of this.
The fish-remains of the Carboniferous formation show a great similarity to those of the preceding. They occur throughout the series, but are very irregularly distributed, being extremely scarce in some countries, whilst in others entire beds (the so-called bone-beds) are composed of ichthyolites. In the ironstones they frequently form the nuclei of nodules, as in the Devonian.
Of Chondropterygians the spines of Onchus and others still occur, with the addition of teeth indicative of the existence of fishes allied to the Cestracion-type (Cochliodus, Psammodus): a type which henceforth plays an important part in the composition of the extinct marine fish faunæ. Another extinct Selachian family, that of Hybodontes, makes its appearance, but is known from the teeth only.
Of the Ganoid fishes, the family Palæoniscidæ (Traquair) is numerously represented; others are Cœlacanths (Cœlocanthus, Rhizodus), and Saurodipteridæ (Megalichthys). None of these fishes have an ossified vertebral column, but in some (Megalichthys) the outer surface of the vertebræ is ossified into a ring; the termination of their tail is heterocercal. The carboniferous Uronemus and the Devonian Phaneropleuron are probably generically the same; and the Devonian Dipnoi are continued as, and well represented by, Ctenodus.
The fishes of the Permian group are very similar to those of the Carboniferous. A type which in the latter was but very scantily represented, namely the Platysomidæ, is much developed. They were deep-bodied fish, covered with hard rhomboid scales possessing a strong anterior rib, and provided with a heterocercal caudal, long dorsal and anal, short non-lobate paired fins (when present), and branchiostegals. The Palæoniscidæ are represented by many species of Palæoniscus, Pygopterus and Acrolepis, and Cestracionts by Janassa and Strophodus.
The passage from the Palæozoic into the Mesozoic era is not indicated by any marked change as far as fishes are concerned. The more remarkable forms of the Trias are Shark-like fishes represented by ichthyodorulithes like Nemacanthus, Liacanthus, and Hybodus; and Cestracionts represented by species of Acrodus and Strophodus. Of the Ganoid genera Cœlacanthus, Amblypterus (Palæoniscidæ), Saurichthys persist from the Carboniferous epoch. Ceratodus appears for the first time (Muschel-Kalk of Germany).