Simple sequence repeat (SSR) markers were used to study the genetic relationship among different strains of Citrus grandis ‘Tomentosa’ and other representative germplasms of Citrus. 175 alleles were amplified with 25 pairs of SSR primers and 15 samples. The results of cluster analyses showed that ‘Tomentosa’ and pomelos were closely related. Some ‘Tomentosa’ materials with homonym are found to be genetically different. High performance liquid chromatography (HPLC) was used to determine the content of naringin in young fruit of different germplasm and fruit tissue of ‘Tomentosa’ with varied diameters. The results showed that the content of naringin in the young fruit of ‘Tomentosa’ was significantly higher than that of Huazhou local pomelo ‘Guangqing’ and common pomelo from other areas,affected by the growing season and environmental factors. With the increase of fruit diameter,the content of naringin in pericarp and pulp of ‘Zhaomao(Wu)’ and ‘Jiaxiyang(Wu)’ decreased,and the content of naringin in pulp was higher than that in pericarp. The results of comprehensively analyzing fruit size and active ingredient content showed that the fruit diameter of 4-8 cm was the suitable harvesting period of ‘Tomentosa’,and the fruit with diameter of 6 cm was optimal for harvesting.