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Next‐generation sequencing (NGS) technologies offer the opportunity for population genomic study of non‐model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene‐coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non‐model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to …