An association genetics approach was used to examine individual genes and alleles at several loci responsible for complex traits controlling wood traits (cellulose, lignin, and 6C sugar) in European black poplar (Populus nigra). Due to fast growth, clonal propagation and availability of genomic resources have allowed us to investigate further genetic control of wood traits in the species. From thirty-nine candidate genes, 384 SNPs were successfully genotyped in a clonally replicated 288 P. nigra clone population. Only 50.5% of these markers were polymorphic that could be used in association mappings. The association population (4 ramets per clone) was phenotyped for cellulose, lignin, and 6C sugar contents. Moderately high heritabilities were observed for cellulose and 6C sugar while it was low in lignin. Furthermore, a moderately strong and positive genetic correlation was found between cellulose and lignin which may hinder genetic improvement in cellulose content due to the correlated response on lignin. The LD, across all candidate genes, showed a rapid decay with physical distance. Single-marker-based association tests using GLM and MLM models were implemented to identify associations for cellulose, lignin, and 6C sugar contents. Eleven unique single marker associations for cellulose, 5 for lignin, and 6C sugar contents were identified from 39 candidate genes, but only one marker for cellulose content (CesA3A-15-456) had a significant association with cellulose and with dominant gene effect after multiple test correction was applied. The percent of total variation explained by significant single marker associations ranged from 3 to 9.2% in cellulose, 2.8 to 3.8% in lignin, and 3.2–5.5% in 6C sugar contents, respectively. Given the rapid decay of within-gene linkage disequilibrium, limitation of sample size, overcorrection for false positives, and intensity of phenotypic selection, it is likely that some of these single marker associations are genuine and deserve to be further investigated with a larger and diverse study population.