The macrophages play an important role in innate immunity in fishes. Ayu (Plecoglossus altivelis) is an economically important fish in Japan and China. Despite many studies, little is known about the ayu macrophage-specific gene expression. Here, we isolated Macrophages from ayu head-kidney. The transcriptomic gene expression profile of ayu macrophages was obtained by illumina sequencing. Ayu macrophage transcriptomes revealed 88160 transcripts. This result allowed us to identify novel gene expression patterns in ayu macrophages.