Sheep dairy sector is a valuable activity in Mediterranean Countries that represents 28% of the world milk production, contributes to maintain the rural population and is the support of a processing sector focused on traditional products. One of the challenges that the sector faces is the fulfillment of hygienicsanitary standards of quality, evaluated within milk quality systems through the standard plate count. Nevertheless, the quality of sheep milk is related to different groups of microorganisms, whose presence have different consequences in milk and milk products. Thus, the aim of the present work has been to investigate the differential microbiological quality of sheep milk from bulk tank and the relationship between the microbial groups. A total of 308 bulk tank milk samples from 77 sheep farms were tested for the microbiological study with the main microbial groups found in milk (standard plate count, thermoduric, and psychrotrophic flora, total coliforms, catalase negative Gram positive cocci, lactic acid bacteria, butyric acid bacteria and coagulase positive staphylococcus). The results of the different microbial groups show that, in general, milk samples collected in this study show an adequate hygienic quality and the counts are distributed around low and intermediate intervals. The study demonstrates the necessity to optimize hygiene (above all, on-farm cleaning and disinfection, refrigeration process and feeding management) and sanitary practices (mastitis protocol), for the control of some microbial groups. In addition, the lack of relationship between standard plate count and some microbial groups with interest in sanitary (coagulase positive staphylococcus) or technological procedures (butyric acid bacteria) informed about the necessity to monitor them in the control systems of sheep milk quality.