Paddy fields in north-eastern Thailand are heterogeneous agro-ecosystems that can be described as mosaics of paddy rice plots, dykes and termite mounds. The aim of this study was to determine if this heterogeneity influences soil macrofauna biodiversity. While biodiversity did not vary as a result of different rice management practices (direct seeding and transplanting), dykes and mounds were vital to the maintenance of soil macrofauna biodiversity. Diversity and density were higher in termite mounds and field dykes, compared to rice plots, especially during the rainy season. Consequently, termite mounds and dykes can be considered to be biodiversity hotspots that behave as refuges for other soil macrofauna during the rainy and dry seasons, providing protection against flooding and dryness. The importance of these patches of biological activity in terms of ecosystem functioning and services are discussed.