High density genetic map are valuable approach for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery for economically agronomic traits in plant species. However, high-resolution genetic maps applied to gene tagging associated with important traits and examined the genomic features underlying recombination landscape in radish (Raphanus sativus) is not well documented. In this study, an ultra-high dense genetic map with 411891 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin color. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions were enriched near gene promoters and terminators. The recombination rate in recombination hot regions was positively correlated with SNPs, gene density and GC content, respectively. Functional annotation indicated that genes within recombination hot regions were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the recombination hot regions. The results provide novel insights into the radish genome evolution, recombination landscape and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish. This article is protected by copyright. All rights reserved.