We tested for associations between single nucleotide polymorphisms (SNPs) in five candidate genes allied with the growth hormone axis and the age-specific growth rate of Arctic charr (Salvelinus alpinus L.: Salmonidae). Two large full sib families (N=217 and 95) were created by backcrossing males that were hybrids between two phenotypically divergent populations from Labrador, Canada and from Nauyuk Lake, Canada to females that were from Nauyuk Lake. Measures of individual growth rate (wet weight and fork length) were made three times during a 420-day period after the juveniles were transferred from 4 to 11 degrees C. We then identified SNP markers in 10 proposed candidate genes known to be related to the growth hormone axis. Comparative alignments of amino-acid sequences and nucleotide sequences from other fish species were used to design PCR primers that would amplify 0.5-3 kb DNA regions of the candidate genes. All the individuals in the two backcross families were genotyped for these SNP markers using either polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) or bidirectional amplification of specific alleles (Bi-PASA) approaches. A significant association between a particular SNP allele and early growth was found for the locus containing the growth hormone-releasing hormone and pituitary adenylate cyclase-activating polypeptide genes (GHRH/PACAP2, P=0.00001). We argue that using comparative sequence information to design PCR primers for candidate genes is an efficient method for locating quantitative triat loci in nonmodel organisms.