Association mapping is a recommended method to dissect the genetic basis of naturally occurring trait variation in non-model tree species with outcrossing mating systems and large population sizes. We report here the results of the first association-mapping study in maritime pine (Pinus pinaster Ait.), a conifer species of economical importance for timber and pulp production in south-western Europe. Two association samples were examined: 160 plus trees belonging to the first generation breeding population (G0, resulting from mass selection for overall good growth and form in the forest of South West of France) and 162 trees from the second generation breeding population (G1, resulting from biparental crosses between G0 trees). These samples were (1) genotyped for 184 in vitro SNPs discovered in 40 candidate genes for plant cell wall formation or drought stress resistance and 200 in silico SNPs detected in 146 contigs from the maritime pine EST database and (2) phenotyped for growth, stem straightness and wood chemistry traits in progeny or clonal experimental designs (from 768 to 5,080 phenotypes depending on the trait). First, SNP data were used to test for putative stratification in the breeding population. Then, two different approaches using pedigree records to account for inbreeding were used to test for associations. Despite the a priori low power of the designs, we identified two mutations that were significantly associated, one with variation in growth (in a HD-Zip III transcription factor) and the other with variation in wood cellulose content (in a fasciclin-like arabinogalactan protein).