A number of Estonian Devonian fishes are shown to be junior synonyms of Scottish species. The Estonian sarcopterygian osteolepid Gyroptychius pauli was originally thought to be closely related to the Scottish species Gyroptychius milleri being differentiated by minor morphological differences of the skull roof. However, here we show that the only skull roof available of G. pauli to the original description (the holotype) was badly damaged in places. This and the fact that skull roofs of osteolepid fishes are morphologically highly variable has allowed us to compare the Estonian and Scottish species and show that G. pauli is a junior synonym of G. milleri. It has also been known for some time that Estonian coccosteid arthrodire Coccosteus orvikui was a junior synonym of the Scottish species Coccosteus cuspidatus. Here we present the evidence for this assumption and also show that the Scottish coccosteid arthrodire Millerosteus minor is almost certainly present in Estonia. Finally, it is shown that the three species have the same stratigraphical distribution in the two regions, strongly indicating a close faunal connection between the Middle Devonian of Estonia and the Middle Devonian Orcadian Basin of Scotland.