One pair of near isonegic yellow/black seeded rape (Brassica napus L) were used as experimental materials to study the changes of lignin contents and enzymes activities of 4-coumarate: CoA ligase (4CL), Cinnamyl alcohol dehydrogenase (CAD) and ferulate 5-hydroxylase (F5H) in seedcoats during the stage of seed development. The variation analysis showed that the changes of lignin contents and enzyme activities of 4CL, CAD and F5H in seed coat had significant differences between black- and yellow-seeded rapes, and also between different development stages. The correlation analysis demonstrated that the lignin contents were positively correlative to the activities of all three enzymes investigated in the study, and the interactions between them in the seed coat of the two lines. For yellow-seeded rape, the correlation coefficient (0.7262018) of lignin content and the interaction between 4CL and F5H was significant, the lignin contents were highly positively correlative to the activities of CAD and F5H, the interaction between 4CL and CAD, and the interaction between CAD and F5H. For the black-seeded rape, only the lignin content was highly positively correlative to the activity of F5H (the correlation coefficient was 0.772949), the other correlation coefficients, i. e. lignin contents to 4CL, CAD activities, the interactions between the three enzymes were not significant although all the correlation coefficients were above 0.5000. The results suggested that 4CL, CAD and F5H regulated the biosynthesis of lignin in seedcoat of rapes,leading to the lignin contents in the seedcoats of the yellow-seeded rape much lower than that of the black-seeded line,and affecting the thickness of the developing seedcoats in rapes. Therefore, it was likely to change the seedcoat ratio by overexpressing or suppressing the activities of one of the enzymes, both of them or all of them.