Alnus glutinosa (L.) Gaertn. and Alnus incana (L.) Moenx. grow naturally in Lithuania, and their ranges overlap. They are considered ecologically and economically important species of forest trees. The objective of our study was to determine plant bioactive compounds, such as total phenolic (TPC) and flavonoid compounds (TFC), in the wood of alders and their hybrids in order to specify the opportunity to use secondary metabolites (SM) for the identification of alder hybrids. The samples from juvenile and mature alder woods (n = 270) were collected at three different sites in the natural forests of Lithuania. The TPC and TFC content was determined using spectrophotometric methods and was expressed in mg/g of fresh mass. Obtained results showed that the TPC of A. incana was statistically higher compared to A. glutinosa; however, in hybrid alder wood it was intermediate. The TFC was statistically higher in hybrid alder wood and lowest in A. glutinosa. The TFC was higher in mature trees; however, the TPC showed the opposite tendency. In our case, the TPC was higher in continental sites, while TFC was higher in mature alders at costal sites. Obtained data allow us to assume that TPC and TFC in alder wood can be used as taxonomic markers. This study expanded the knowledge of alder physiology and contributed to the identification of alder hybrids. The correct identification of tree species is very important for the conservation of natural resources and for the sustainable use of higher value-added products.