Apolipoproteins, the protein moieties of lipoproteins, participate in physical activities in different forms. A 14 kDa apolipoprotein (Apo-14 kDa) and apolipoprotein E (ApoE) are thought to be associated with embryonic development in animals. We analyzed the gene structure and phylogenetic evolution of these two types of apolipoprotein in the common carp (). In addition, we documented the pattern of expression using RT-PCR to provide insight into their function during the embryonic development of carp. , including and (identity=90%). Phylogenetic analysis revealed that Apo-14 kDa-a has a close relationship with that of most other teleosts and that Apo-14 kDa-b has the closest relationship with that of differentiation of the family yprinidae, although ApoE is characterized by four homologous genes. The expression of carp was highest in the liver and head-kidney, was very low in the intestine, and undetectable in the remaining tissues. Conversely, we were only able to detect expression of in the liver. We observed tissue specific differences in the expression of were only detected in the intestine whereas were present in the brain, skin, gill, liver, spermary, intestine, heart, muscle, body-kidney, and head-kidney. in the ovary. Our observations suggest there is considerable variation in the expression and function of . Furthermore, qRT-PCR analysis suggests that the expression of these six genes varies throughout embryonic development, both within and among genes. This is consistent with the molecular phylogeny of these genes. qRT-PCR analysis suggests that play an important role throughout different stages of embryonic development in common carp.