Backfat thickness is one of the most important traits of commercially raised pigs. Meishan pigs are renowned for having thicker backfat than Landrace pigs. To examine the genetic factors responsible for the differences, we first produced female crossbred pig lines by mating Landrace (L) × Large White (W) × Duroc (D) females (LWD) with Landrace (L) or Meishan (M) boars (i.e., LWD × L = LWDL for Landrace offspring and LWD × M = LWDM for the Meishan offspring). We confirmed that LWDM pigs indeed had a thicker backfat than LWDL pigs. Next, we performed gene expression microarray analysis in both genetic lines to examine differentially expressed genes (DEGs) in energy metabolism-related tissues, subcutaneous adipose (fat), liver, and longissimus dorsi muscle tissues. We analyzed the annotation of DEGs (2-fold cutoff) to functionally categorize them by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The number of DEGs in muscle tissues of both lines was much less than that in fat and liver tissues, indicating that DEGs in muscle tissues may not contribute much to differences in backfat thickness. In contrast, several genes related to muscle (in fat tissue) and lipid metabolism (in liver tissue) were more upregulated in LWDM pigs than LWDL pigs, indicating that those DEGs might be responsible for differences in backfat thickness. The different genome-wide gene expression profiles in the fat, liver, and muscle tissues between genetic lines can provide useful information for pig breeders.