The evolutionary dynamics of the 4CL gene encoding 4-coumarate:coenzyme A ligase was investigated in the genus Larix (Pinaceae) by comparing copy number, GC content and codon usage, sequence divergence, and phylogenetic analysis. All 4CL clones of Larix formed a strongly supported monophyletic group, in which two robust clades (4clA and 4clB) derived from an ancient gene duplication event in the common ancestor of Larix were identified. Further gene duplication in the 4clA clade gave rise to two subclades 4clA(1) and 4clA(2). Frequent duplication/deletion appears to be a common evolutionary phenomenon in the 4CL gene family and paralogous genes differ greatly in their evolution rate. The existence of L. speciosa in subclades 4clA(1) and 4clA(2) suggests that this species may represent a primitive form of Larix or the closest relative of the common ancestor of the Eurasian Sect. Multiserialis. In addition, cpDNA and nrDNA ITS analyses support the hypothesis of an early separation of Larix into a North American and a Eurasian clade, which is congruent with the results of previous allozyme and very recent AFLP analyses. The unexpected close relationship between North American larches and the short-bracted species L. gmelinii in East Asia, based on the 4CL gene tree, may stem from lineage sorting.