NGS data for four invertebrates: Amphinemura sulcicollis, Isoperla grammatica, Baetis rhodani and Oniscus asellus.

A low-coverage genome was generated for each of four environmental key-species of macroinvertebrate taxa for the purposes of microsatellite marker development. As widespread and functionally important organisms, which are often neglected in favour of studies on vertebrates, this data will be a useful resource for further research.