During a survey of freshwater diatoms from Mojiang River, Chebaling Nature Preserve in Shaoguan City, Shixing County, Guangdong Province, China, a new Encyonema species, Encyonema chebalingense sp. nov., was discovered. Based on observations with light and scanning electron microscopy, a detailed morphological description of E. chebalingense is here presented. The main features of E. chebalingense include: conspicuously asymmetrical and dorsiventral, semielliptical to semielliptical–lanceolate valves, with a filiform raphe; dorsal margin clearly arched and ventral margin nearly straight or slightly concave; central area on the ventral side formed by 1–2 shorter central striae; and short tectullae projecting within the striae. The new species was compared with some similar species, all of which show similarities to E. chebalingense but differ in features such as dimensions, internal valve structure, stria density and valve shape. This genus is common and abundant in relatively clean waters, and other new species most likely will be recorded in the future from China.