We isolated and characterized the full-length cDNA sequences of nine apolipoproteins (apoA-I-1, apoA-I-2, apoA-IV, apoE-1, apoE-2, apoC-I, apoC-II, apo-14 kDa, and apoM) in the Korean spotted barbel Hemibarbus mylodon (Teleostei: Cypriniformes), an endangered fish species. Nucleotide sequences of all apolipoproteins of H. mylodon showed high levels of identity to those of cyprinid species. The secondary structures of their deduced amino acid sequences were generally conserved with previously reported vertebrate counterparts. Molecular phylogenetic analyses revealed that apolipoproteins from teleosts and avian/mammalian species were phylogenetically separated according to each encoded protein. Within each apolipoprotein lineage, teleosts consistently formed a strongly supported monophyletic group and were genetically separated from terrestrial vertebrates. Tissue distributions of apolipoprotein transcripts in H. mylodon were variable depending on apolipoprotein family members with relatively high expression levels in the liver and intestine. The overall spectrum of mRNA tissue distribution was wider in H. mylodon than in other teleosts and mammals. In addition, our findings showed the multiple isoforms of apoA-I and apoE were differentially modulated across tissues possibly with an isoform-specific role in a given tissue.