Cuticluar hydrocarbons (CHCs) are a ubiquitous component of insect cuticles that are used for a wide range of chemical signaling functions, especially recognition. Recognition and other signals are vital for the maintainance of insularity and cooperation in social insect colonies. Therefore, we expect natural selection on the composition and variabitlity of social insect CHC profiles. Selection on these signals may result in the evolution of genetic polymorphism affecting variations in CHC profiles. Here we tested for a genetic basis of CHC variation in the desert ant Cataglyphis niger. We applied a genomic mapping appraoch to a cohort of brothers from the same nest to reduce noise from environmental effects and achieve a clear statistical signal for association between CHCs and quantitative trait loci (QTL). This analyses identified 19 QTLs associated with 8 our of 31 tested CHCs, and one QTL associated with total CHC quantity. These QTLs are located on 11 different chromosomes, including some where QTLs of different CHCs overlap. Each QTL explains between 13-25% of the CHC variation. We highlight several candidate genes in the QTLs identified, including fatty acid elongase and reductase genes. Our results reveal a polygenic genomic architecture underlying CHC variation in ants and open new research avenues into the genetic basis and evolution of chemical signaling in social insects.