Animal assemblages associated with macrophytes in shallow waters have been studied intensively in different parts of the world. However, there is a paucity of ecological studies on algae-associated microscopic animals while there are numerous studies on meio/macro benthic organisms. The present study focused not only on meio- but also micro-benthos associated with Sargassum thunbergii, one of the most common intertidal algae in Japan. Samples of Sargassum and associated organisms were collected from three different intertidal zones. Algal morphology was quantified by measurement of fractal dimension, D, and the abundances of different animal taxa were analysed in relation to D values and intertidal height. Among different taxa, ostracoda and nauplii stages were affected by D values and intertidal height; mollusks, foraminiferans, amphipod, arthrostraca and mobile polychaetes were affected by intertidal height only, while copepoda and sessile polychaetes were affected by neither. These results showed that algal morphology and intertidal height can both affect animal abundances and species composition in different ways.