New occurrences of codiacean algae, some definitely referable to Garwoodia gregaria (Nicholson), and algal stromatolites are described from the Manlius Limestone Formation of central and eastern New York. This is the first report of codiaceans from the Devonian of the U.S., and the occurrence of Garwoodia extends the time of first appearance of this genus from early Carboniferous to early Devonian. The algal stromatolites are thin, irregular, carbonate laminations on skeletal debris, intraclasts, or the sedimentary substrate, presumably formed by encrusting blue-green algal mats. The mutual exclusiveness of Manlius stromatolites and codiaceans as well as their dissimilar lithologic and faunal associations suggest environmental differences between lower Manlius deposits (with stromatolites) and upper Manlius deposits (with codiaceans). The former are interpreted as tidal flat or very shallow lagoonal sediments having an impoverished fauna, mud cracks, ripple marks, limestone-pebble conglomerates, and encrusting blue-green algae; the latter are relatively deeper water, lagoonal sediments with a diverse benthos, small patch reefs or bioherms, and abundant codiaceans.