Liver-type fatty acid-binding protein (L-FABP) is a member of intracellular lipid-binding proteins involved in the transportation of fatty acids. We detected the polymorphisms of duck L-FABP gene and its association with the intramuscular fat (IMF) and other fat-related traits. The complete sequence of duck L-FABP gene (four exons and three introns, 2,542 bp) was obtained in this study. The polymorphism of L-FABP gene was examined with direct DNA sequencing method in 231 individuals from different breeds, and a novel single nucleotide polymorphism in the exon 3 was detected. The polymorphism was shown to be associated with the contents of C16:0, C18:3 and the total IMF in pectoral muscle. The content of C16:0 in genotype CC was significantly higher than CT (P < 0.01) and TT (P < 0.01), and the genotype CT was higher than TT (P < 0.01). The content of C18:3 in genotype TT was significantly higher than CC and CT (P < 0.01), whereas the genotype CC and CT had no significant difference (P > 0.05). The content of IMF in genotype CC was significantly higher than CT (P < 0.01). However, no significant difference was detected between genotype CC and TT or genotype CT and TT (P > 0.05).