The recent democratization of next-generation-sequencing-based approaches towards nonmodel species has made it cost-effective to produce large genotyping data sets for a wider range of species. However, when no detailed genome assembly is available, poor knowledge about the organization of the markers within the genome might hamper the optimal use of this abundant information. At the most basic level of genomic organization, the type of chromosome (autosomes, sex chromosomes, mitochondria or chloroplast in plants) may remain unknown for most markers which might be limiting or even misleading in some applications, particularly in population genetics. Conversely, the characterization of sex-linked markers allows molecular sexing of the individuals. In this study, we propose a Bayesian model-based classifier named detsex, to assign markers to their chromosome type and/or to perform sexing of individuals based on genotyping data. The performance of detsex is further evaluated by a comprehensive simulation study and by the analysis of real data sets from various origins (microsatellite and SNP data derived from genotyping assay designs and NGS experiments). Irrespective of the origin of the markers or the size of the data set, detsex was proved efficient (i) to identify the sex-linked markers, (ii) to perform molecular sexing of the individuals and (iii) to perform basic quality check of the genotyping data sets. The underlying structure of the model also allows to consider each of these potential applications either separately or jointly.