The spatial zonation of macrofauna in the core region of Zhanjiang Mangrove Nature Reserve (located along coastal areas of the Leizhou Peninsula, Guangdong, China) was studied with two transects vertical to the shoreline. The first transect was near Deyao village where Assiminea lutea, Macrophthalmus erato, Paracleistostoma depressum, Cleistostoma dilatatum, Littoraria melanostoma, Ceratonereis burmensis, Uca arcuata, and Pseudoringicula sinensis were found to be dominant species of the macrofauna. Along this transect, three faunal zones of the mangrove swamp could be divided from the high to low tide part: The Assiminea lutea Uca arcuata Paracleistostoma crassipilum zone, the Cleistostoma dilatatum Macrophthalmus erato Littoraria melanostoma zone, and the Paracleistostoma depressum Cerithidae cingulata zone. Molluscs and crustacean exhibited highest individual density in this transect. Molluscs also mainly influenced the dynamics of community biomass, as well as the species diversity index. In the second transect near Hongzhai village, the dominant species of the macrofauna species included Assiminea lutea, Upogebia sp., Paracleistostoma depressum, Cleistostoma dilatatum, a species beloning to the family Ellobiidae, Littoraria melanostoma, Pseudoringicula sinensis, Parapenaeopsis hardwickii, Uca arcuata, and Ceratonereis burmensis. Four faunal zones could be determined in this section: The Littoraria melanostoma Pseudoringicula sinensis Ceratonereis burmensis zone, the Assiminea lutea Cleistostoma dilatatum zone with a dominant species belonging to the Ellobiidae, the Upogebia sp. Paracleistostoma depressum zone, and the Metaplax sheni Cerithidae cingulata zone. The crustacean showed highest individual density in this transect. Similar to the Deyao transect, dynamics of community biomass and the species diversity index of the Hongzhai transect were mainly influenced by molluscs. By hierarchical clustering and non-metric multi-dimensional scaling, the macrofauna communities could be divided into 3 and 4 groups in the Deyao and Hongzhai transect, respectively. These groups corresponded to the different vegetation types of the mangrove swamp. Taken together, our observations indicate that the spatial zonation of the macrofauna was mainly affected by characteristics of the mangrove community, sediment characteristics and the tidal line.