Open-pollinated hybridisation seed orchards of European and Japanese larches produce mixed progenies combining a highly variable proportion of hybrids along with pure parental species. For several reasons, it is desirable to identify and to sort out hybrids from pure species at the seedling stage. Taxa identification of 1–2 yr-old seedlings was attempted using non-destructive assessment of several traits, including morphology, phenology, growth and architecture parameters. Two sets of progenies originating from 10 open-pollinated hybridisation seed orchards were used, relying in a first step on taxa identification of individual seedlings with diagnostic molecular markers. Based on 21 traits assessed, some clear trends in pure species and hybrid features were apparent but due to the large and overlapping ranges of taxa characteristics, no single parameter allowed unambiguous identification of taxa. Combination of traits through linear discriminant analysis made possible correct classification of 90.2% to 98.6% of individuals depending on the orchard although there were a few problematic orchards. Two traits appeared particularly pertinent for discriminating young plants taxa, namely 1st-yr leaf retention (marcescence) and the bark colour of 2nd-year shoot increments. Results were corroborated using progenies from several orchards and over two experimental periods.