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Miniature inverted-repeat transposable elements (MITEs) are a group of DNA transposable element (TE) which preferentially distributed with gene associated regions. Tens of MITEs families have been revealed in Brassica napus genome, they scatter across the genome with tens of thousands copies and produce polymorphisms both intra-and inter-species. Our previous studies revealed a Tourist-like MITE, Monkey King, associated with vernal-ization requirement of B. napus, however there are still few studies reveal MITE association with agricultural traits in B. napus.In the present study, 80 polymorphic markers were developed from 55 MITEs, and used to evaluate genetic diversity in a panel of B. napus accessions consisting of 101 natural and 25 synthetic genotypes. Five agricultural traits, oil content, glucosinolate content, erucic acid content, weight of thousand seeds (WTS) and plant height, were investigated across 3-years field experiments, in addition, two traits, hypocotyl length and root length, were evaluated at the 4-leaf stage in the laboratory. Correlations between the MITE-based markers and seven traits were analyzed, finally, 10 polymorphic markers produced by 6 pairs of MITE specific primers were revealed relatively high correlation with 5 traits. Two polymorphic markers were anchored with two candidate genes, BnaA02g13530D and BnaA08g20010D, respectively, which may contribute to glucosinolate content and WTS. This research may contribute to genetic improvement through utilization of MITE-induced polymorphisms in Brassica species.