The composition of bee-collected pollen (BCP) significantly depends on its botanical and geographical origin. In this context, providing information about compounds considered as potential chemotaxonomic markers is useful. The current study aimed to compare the phytochemical profiles of two BCP samples with the same botanical origin (Brassica napus) collected in Serbia and Türkiye. Both samples were monofloral ensuring mostly consistent chemical composition. In total, fifty-one and thirty-eight compounds were identified in Turkish and Serbian BCP, respectively, using untargeted UHPLC Q-ToF MS analysis. The identified phytochemicals included phenolics (phenolic acids and flavonoids derivatives), phenylamides, and glucosinolates. By comparing the findings with literature data, four flavonol glycosides (in particular kaempferol) can be considered as potential chemotaxonomic markers for rapeseed BCP. However, the current research revealed phenylamides as much more characteristic compounds in BCP with higher chemotaxonomic potential. Namely, eight spermine derivatives were identified as potentially characteristic for Brassica pollen. This study is the first to report phenylamides as potential chemotaxonomic markers in BCP.