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Simple Summary: In a previous study, 30 SINE-RIPs were applied for population genetic analysis in 7 Chinese miniature pig populations and approved effectively in the genetic distances and breed-relationships between these populations. There are abundant indigenous pigs famous across the world for their prolificacy in the Jiangsu Province of eastern China, such as Meishan, Erhualian. Since pork production relies on limited commercial breeds such as Landrace, Large White, and Duroc pigs, characterized by maximizing productivity in intensive production systems, these indigenous pigs are nowadays decrease sharply. The genetic characterizations of these resources are essential requirements for the development of conservation, selection, and sustainable utilizations. Therefore, SINE-RIPs were selected to evaluate the genetic variation and population structure of Jiangsu pig populations and the results may assist with the conservation and utilization of these native pig populations. Short interspersed nuclear elements (SINEs), one type of retrotransposon, are considered to be ideal molecular markers due to their wide distribution in the genome, high copy number, and high polymorphism. Preliminary studies have identified more than 35,000 SINE-retrotransposon insertion polymorphisms (RIPs) in the pig genome. In this study, 18 SINE-RIPs were used to evaluate the genetic variation and population structure of seven native pig populations and two crossbreeds in the Jiangsu Province of China. Two commercial pig breeds (Duroc and Large White) and one Italian native breed (Sicilian Black pig) were selected as the control. The results showed that all 18 SINE-RIPs were polymorphic among these pigs. The Jiangsu native pig populations (Erhualian, Fengjing, Middle Meishan, Mi, Shawutou, Small Meishan, and Huai) were shown to be more polymorphic than the crossbreeds (Sushan and Sujiang) and external breeds (Sicilian Black pig, Large White, and Duroc) based on the expected heterozygosity and polymorphic information content values. Some native pigs, including Small Meishan, Mi, Middle Meishan, and Erhualian, had a higher degree of inbreeding according to the FIS values. Based on the neighbor-joining tree, all of the Jiangsu native pig populations formed one branch, while the three external pig breeds formed the other branches, with the two crossbreeds containing more than 50% external pig ancestry. The Huai pigs were independent of the other Jiangsu native pigs but shared a common ancestor with Sujiang and Mi. The results provide a new perspective on the population structure of these native pig breeds and will assist with the conservation and utilization of Chinese native pigs. [ABSTRACT FROM AUTHOR]