Accompanying archive for the manuscript 'Prevalence and distribution of two polycipiviruses in wild black garden ants (*Lasius niger* L.) in the Netherlands'. In this study, we investigated the prevalence and genetic diversity of Lasius niger virus 1 (LniV-1) and Myrmica scabrinodis virus 1 (MsaV-1) in wild colonies of the black garden ant (Lasius niger L.) across the Netherlands. We surveyed 40 wild L. niger colonies, sampled at geographically distinct locations, using RT-PCR to assess viral prevalence and genetic diversity. Viral prevalence was estimated at both colony and individual levels. Amplicons were sequenced to explore potential correlations between geographic distribution and genetic diversity for both viruses. In addition, complete or almost complete viral genome sequences were obtained and assembled for one MsaV-1 genome from Groningen, The Netherlands, and one MsaV-1 and one LniV-1 from Vienna, Austria.