Turnip (Brassica rapa ssp. rapa) and ‘Daikon’ (Raphanus sativus) are major vegetative crops in Asia, particularly in Japan. In these vegetables, wide morphological variations are observed in the roots of local and commercial cultivars, for instance thickness, shape, length and color. Thickness is the most important trait in them. The objective of this study is to find quantitative trait loci (QTL) for root thickness in turnip and Daikon using F2 populations derived from crosses of thick root cultivars ( inbred lines from turnip ‘Shogoin’ in B. rapa and Daikon ‘Aokubi’ in R. sativus) and thin root cultivars ( inbred lines from Chinese cabbage ‘Chiifu’ in B. rapa and Daikon ‘Sayatori’ in R. sativus). In these F2 populations, we measured maximum diameter of the roots as phenotype data, and constructed genetic linkage maps using dot-blot SNP markers designed from R. sativus EST sequence data. QTLs for root thickness were analyzed using the phenotype data. Four QTLs were found on four different linkage groups (LGs) in turnip, and four QTLs were found on three different LGs in Daikon. Comparison of QTLs between two species using our Daikon genome sequence data and the public B. rapa genome sequence data revealed two syntenic regions to have genes controlling root thickness.