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Black and red raspberries (<i>Rubus occidentalis</i> L. and <i>Rubus idaeus</i> L.) are the prominent members of the genus <i>Rubus</i> (Rosaceae family). Breeding programs coupled with the low costs of high-throughput sequencing have led to a reservoir of data that have improved our understanding of various characteristics of <i>Rubus</i> and facilitated the mapping of different traits. Gene <i>B</i> controls the waxy bloom, a clearly visible epicuticular wax on canes. The potential effects of this trait on resistance/susceptibility to cane diseases in conjunction with other morphological factors are not fully studied. Previous studies suggested that gene <i>H</i>, which controls cane pubescence, is closely associated with gene <i>B</i>. Here, we used tunable genotyping-by-sequencing technology to identify the <i>de novo</i> SNPs of <i>R. occidentalis</i> and <i>R. idaeus</i> using an interspecific population that segregates for the waxy bloom phenotype. We created linkage maps of both species and mapped the identified SNPs to the seven chromosomes (Ro01–Ro07) of <i>Rubus</i>. Importantly, we report, for the first time, the mapping of gene <i>B</i> to chromosome 2 of <i>R. occidentalis</i> using a genetic map consisting of 443 markers spanning 479.76 cM. We observed the poor transferability of <i>R. idaeus</i> SSRs to <i>R. occidentalis</i> and discrepancies in their previously reported chromosome locations.