The concept of a core parent was proposed by breeders to describe elite lines with both good field performance and high potential for breeding superior new lines. Guichao 2 is one of the most important rice core parents in China. In the present study, Simple Sequence Repeat marker (SSR) based genome-wide screening was performed for Guichao 2, its parents and derivatives to study the genetic diversity and structure of them. A total of 348 polymorphic markers and 833 polymorphic alleles were detected. The Polymorphic Information Content (PIC) value ranged from 0.15 to 0.95 and averaged 0.39. Genetic similarity among the ten varieties varied from 0.751 to 0.926 with an average of 0.842, indicating that the genetic diversity is not abundant. At the whole genome level, Chaoyangzao 18 (30.4%) contributed many more genetic components to Guichao 2 than Guiyangai 49 (16.3%) did. The amount of genetic material transmitted by Guichao 2 to its derivatives varied from 49.7% (Qingliuai) to 59.5% (Fengqingai), with an average of 54.7%. In addition, 78 genomic regions of Guichao 2 were identified as stably inherited by these derivatives, with contribution ratios ranging from 14.29 to 85.71%, with an average of 47.25%. Ten of these regions with the same contribution ratio of 85.1% (RM3412-RM140, RM1339-RM1068, RM6997-RM6172, RM3524-RM3042, RM1388-RM1136, RM1353-RM1243, RM5508-RM3753, RM3395-RM3662, RM3662-RM44 and RM6643-RM2915) were found to be significantly important in the derivative cultivars.