The wild honey bee population in Ireland is an important genetic resource of Apis mellifera mellifera, a honey bee subspecies that is threatened, endangered, or extinct across much of its original range (Western Europe). Due to intensive apicultural practices in Europe, and the global trade in a few highly bred honey bee lines, honey bee populations across Europe are at risk of becoming genetically homogenized reducing their ability to adapt to new threats (e.g. environment, pathogens). Despite the reporting of honey bee colonies in wild habitats in recent years in Europe most do not become established, and self-sustaining populations are unconfirmed. Here we present the monitoring of hundreds of wild colonies by citizen scientists and the research team. To avoid the risk of reporting continued activity when a colony has in fact died out, we applied a standardised monitoring protocol, recording activity four times each year at key points in the honey bee life cycle. We supported citizen scientists with a web-based monitoring platform and a social media community. Using a genomic approach we confirmed the persistence of honey bee lineages at nest sites over a multi-year period. The longest confirmed to date is >5years with the great granddaughter of the original queen present in the nest. We have also identified where new lineages have taken up residence at nest sites. Both genomic and monitoring data is applied to identify adaptive traits which can be used to advocate for the importance of protecting this unique genetic resource for its own sake and for sustainable beekeeping practices.