• body colouration;
  • conservation genetics;
  • management;
  • phenotype;
  • spotting pattern;
  • tree model classification

Five qualitative and seven quantitative colouration and spotting pattern features were measured in 23 brown trout Salmo trutta populations and two hatchery stocks. Simultaneously, the LDH-C1*, a diagnostic locus fixed for *90 and *100 alleles in stocking and native populations from southern Europe, respectively, was analysed to classify the brown trout studied according to their origin: native, hatchery stock and hybrids. The three genotypes showed significant differences in the colouration and spotting features and a discriminant function analysis could correctly identify 79% of the individuals. The most discriminating variables were dorsal fin margin colour, number of opercular spots, presence of the preopercular mark and diameter of black spots. Given the low cost, ease and possibility of field identification of native fish, the results indicate great opportunities for the application of morphological-based classification models on the conservation and management of native brown trout stocks.