Phosphogypsum (PG) is an industrial waste composed mainly by sulphate, turning it a suitable sulphate source for sulphate-reducing bacteria (SRB). In the present work the capability of two SRB communities, one enriched from Portuguese PG (culture PG) and other from sludge from a wastewater treatment plant (culture WWT-1), to use sulphate from PG, was compared. In addition, the impact of this sulphate-rich waste in the microbial community was assessed. The highest efficiency in terms of sulphate reduction was observed with culture WWT-1. The bacterial composition of this culture was not significantly affected when sodium sulphate from the nutrient medium was replaced by PG as sulphate source. Next generation sequencing (NGS) showed that this community was phylogenetically diverse, composed by bacteria affiliated to Clostridium, Arcobacter and Sulfurospirillum genera and by SRB belonging to Desulfovibrio, Desulfomicrobium and Desulfobulbus genera. In contrast, the bacterial structure of the community enriched from PG was modified when sodium sulphate was replaced by PG as sulphate source. This culture, which showed the poorest performance in the use of sulphate from PG, was mainly composed by SRB related to Desulfosporosinus genus. The present work provides new information regarding the phylogenetic characterization of anaerobic bacterial communities with the ability to use PG as sulphate donor, thus contributing to improve the knowledge of microorganisms suitable to be used in PG bioremediation. Additionally, this paper demonstrates that an alternative to lactate and low-cost carbon source (wine wastes) can be used efficiently for that purpose.