Two‐dimensional comprehensive gas chromatography (GC×GC) coupled with mass detection was used as a tool for biosynthetic studies of bumblebee pheromones. Prior to biosynthetic experiments, the chromatographic behaviour of isotopically modified esters in the GC×GC system as well as their behaviour in mass detection was studied. The male marking pheromones of Bombus lucorum, Bombus lapidarius and Bombus terrestris were investigated. Main pheromonal components are ethyl tetradec‐9‐enoate (53 %) and ethyl dodecanoate (6 %) in B. lucorum, hexadec‐9‐en‐1‐ol (52 %) and hexadecan‐1‐ol (31 %) in B. lapidarius, and 2,3‐dihydrofarnesol (58 %) and ethyl dodecanoate (15 %) in B. terrestris. The research strategy was based on 1) in vivo incubation of isotopically (2H, 13C) modified fatty acids (FAs) and analysis of their metabolites and 2) feeding experiments with 2H‐ and 13C‐labelled FAs mixed with food. It was observed that labelled FAs were modified into the most abundant aliphatic compounds present in labial gland secretions. In feeding experiments, the labelled FAs were transformed into pheromone components. Transport of the FA precursors from the fat body through haemolymph was confirmed. The results show that FAs, stored in the form of triacylglycerols in the fat body, are likely to participate in the biosynthesis of some aliphatic pheromone components.