Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology. Transcriptome sequencing in particular has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for NGS methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 sequences with evidence of homology to venom proteins were also discovered. After identifying more than 3,000 putatively orthologous sequences across all six taxa, comparative analyses using multiple methods revealed evidence for positive selection in up to 229 of these orthologs. In addition, between ~ 400 and 1,100 unique orphan genes were found to be present in each congeneric lineage. These sequences exhibited elevated rates of amino acid substitution, consistent with previous hypotheses suggesting that orphan genes may be involved with lineage-specific adaptive evolution.