Background/Question/Methods We are interested in the use of ecological theory derived from macro-organisms distribution and its application on bacterial community composition. The Cuatro Cienegas basin (CCB), located in the Chihuahuan desert, is an ideal study model: it has many aquatic systems that differ quite dramatically in water chemistry, flow rate, size and volume. Furthermore, the basin is a RAMSAR and a UNESCO World Biosphere Reserve that supports ground water-dependent ecosystems with microorganisms new to science and more than 70 endemic macroorganisms, however, agricultural development and associated water extraction in the region have placed new pressures on the ecological integrity of this unique ecosystem. Hence, it is necessary to understand the complex flow system in the area. Since bacterial profiles have shown to be a good indirect indicator of flow systems in the valley we sampled different water sources at a wide area, within a radius of 180 km in and out of CCB using a molecular method (TRFLPs of 16S RNA gene). Results/Conclusions We found that the genetic similarity of some of the samples is related to geographic distances and also to environmental factors, mainly pH. Our results showed that this distribution patterns in the prokaryote communities analyzed are similar to those found for animals and plants. We also show evidence that supports the notion that different ecosystems harbor unique microbial populations, and cosmopolitan species (OTUs in this case) are not common. Understanding these patterns of community structure on bacteria itxs important since their application is becoming essential for effective long-term development and management. Since similarity of sample composition supports that regional flow provides water to springs in CCB (in agreement with recent geological evidences), regional water should be regulated.