The black poplar, the predominant poplar cultivars in China, has substantial economic and ecological importance. However, there were differences in phenotypic traits, such as growth, wood properties, resistance, tolerance and so on, between different black poplar cultivars. So, this study examined the effects of genetic background on the metabolite and volatile compound compositions of black poplar via metabolomics and gas chromatography‒mass spectrometry (GC‒MS). In total, 699 metabolites and 146 volatile compounds were identified. Multivariate statistical analysis revealed that 19-Hydroxy-Pge2, Isopropyl Apiosylglucoside, 3-Hydroxyisoheptanoic Acid, Capsianoside V, 3-(3,4-Dihydroxybenzyl)-7-Hydroxy-5-Methoxy-4-Chromanone, Lysope (0:0/20:0), N-(3-Methylbutyl) Acetamide, and 1,4-Benzothiazine-O-Quinonimine serve as biomarkers for differentiating various black poplar cultivars. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that galactose metabolism, alpha-linolenic acid metabolism, sphingolipid metabolism, and alanine, aspartate, and glutamate metabolism were key metabolic pathways impacting the physiological functions of black poplar. Volatile compound analysis indicated significant variability among the black poplar types
however, all shared (+)-cedrol as the primary odor contributor, which has a cedarwood-like aroma that is woody, dry, sweet, and soft. Most of biomarkers and volatile compounds are the physiological or ecological benefits, can be used to predict complex phenotypic traits of black poplar, offering a solid basis for breeding fine varieties of poplar. The screening approach used here may also be applied to the identification and improvement of other tree cultivars.