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Background  The majority of the subspecies of  Daucus carota  have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the  D. carota  complex.    Results  We used GBS to obtain SNPs covering all nine  Daucus carota  chromosomes from 162 accessions of  Daucus  and two related genera. To study  Daucus  phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of  D. carota , we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2 n  = 18 chromosome from all other species. Our results place all cultivated carrots ( D. carota  subsp.  sativus ) in a single clade. The wild members of  D. carota  from central Asia were on a clade with eastern members of subsp.  sativus . The other subspecies of  D. carota  were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco.  Daucus carota  subsp.  maximus  was discriminated, but neither it, nor subsp.  gummifer  (defined in a broad sense) are monophyletic.    Conclusions  Our study suggests that (1) the morphotypes identified as  D. carota  subspecies  gummifer  (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of  D. carota , (2)  D. carota  subsp.  maximus , on two clades with some accessions of subsp.  carota , can be distinguished from each other but only with poor morphological support, (3)  D. carota  subsp.  capillifolius , well distinguished morphologically, is an apospecies relative to North African populations of  D. carota  subsp.  carota , (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in  Daucus .    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0806-x) contains supplementary material, which is available to authorized users.

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)