To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs, 259 pigs from six populations were genotyped using single-nucleotide polymorphism (SNP) BeadChips.  Principal component analysis (PCA), effective population size (Ne), linkage disequilibrium (LD), and signatures of selection were explored and investigated among the six pig populations.  The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago.  The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations, while it was 0.32 for the Duroc population.  However, the LD of all six pig populations showed the opposite order at long distances (>5 Mb).  Furthermore, 15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs, while eight potential signatures of selection associated with growth traits were detected in Duroc pigs.  Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.