<b>Results:</b> The genomic landscape exhibited that the most commonly altered genes in HCC were <i>TP53</i>, <i>FAT3</i>, <i>PDE4DIP</i>, <i>KMT2C</i>, <i>FAT1</i>, and <i>MYO18A</i>, while <i>TP53</i>, <i>FAT1</i>, <i>FAT3</i>, <i>PDE4DIP</i>, <i>ROS1</i>, and <i>GALNT11</i> were frequently altered in ICC; notably, <i>KRAS</i> (18.18% vs. 1.29%) and <i>BAP1</i> (13.64% vs. 1.29%) alterations were significantly more prevalent in ICC. Here, FAT1 is linked to intrahepatic cholangiocarcinoma.