‘Minihongyou’, a new pummelo mutant was used as material in this study. Morphological survey, SEM (scan electron microscopy) observation and ISSR molecular marker technology were conducted to confirm the taxonomic status of ‘Minihongyou’. (1) According to morphological survey results, the ‘Minihongyou’ fruit is similar with ‘Duncan grapefruit’, but there were a great of differences between ‘Minihongyou’ and ‘Guanximiyou’. Moreover, morphology of young leaves of ‘Minihongyou’ was different from ‘Guanximiyou’ and ‘Duncan grapefruit’. (2) The scanning electron microscopy results showed that pollen size and exine mesh of ‘Minihongyou’ were distinct with ‘Guanximiyou’ and ‘Duncan grapefruit’, howerver, the apertures were the same with the other two species. (3) The cluster results indicated that ‘Minihongyou’ could be classified into the same group with ‘Duncan grapefruit’ in a little genetic distance, which means the genetic relationship between ‘Minihongyou’ and ‘Duncan grapefruit’ was closer than that with other species. It was concluded that ‘Minihongyou’ was a novel pummelo, which was different from ‘Guanximiyou’ and ‘Duncan grapefruit’.