Microborings of endolithic organisms (e.g. algae, fungi) provide valuable indicators of paleoenvironments. The present study documents the distribution of microborings in fossil skeletal substrates from a spectrum of shelf to basinal facies in the Middle Devonian of New York. Endolithic boring in brachiopod shells and corals were prepared using special embedding‐casting method and were examined and photographed with SEM. About 13 distinct types of microborings were discovered, presumably produced by microorganisms (pro‐ and eukaryotic), sponges, bryozoans and worms. Brachiopod holdfast etchings are reported for the first time from Paleozoic rocks. Microborings are non‐randomly distributed among Middle Devonian facies. The highest diversity and abundance of borings occurs in diverse brachiopod and coral‐bearing calcareous mudstones; which appear to represent shallow, well‐aerated and low turbidity environments. Microboring diversity and frequency decreases markedly into mudstones and siltstones recording higher turbidity as well as into dark gray to black basinal shale facies. ‘Leiorhynchus’ brachiopods from probable deeper water, dysaerobic environments display very low diversity of micro‐boring assemblages. They include brachiopod pedicle borings and one endolith which shows similarities to a modem cyanobacterium. If the latter is correctly identified, it brackets all of the studied facies within the photic zone.