Host-specific Bacteroides-Prevotella 16S rRNA genetic markers are promising alternative indicators for identifying the sources of fecal pollution because of their high abundance in the feces of warm-blooded animals and high host specificity. However, little is known about the persistence of these genetic markers in environments after being released into environmental waters. The persistence of feces-derived four different host-specific Bacteroides-Prevotella 16S rRNA genetic makers (total, human-, cow-, and pig-specific) in environmental waters was therefore investigated at different incubation temperatures (4, 10, 20, and 30 degrees C) and salinities (0, 10, 20, and 30 ppt) and then compared with the survival of conventional fecal-indicator organisms. The host-specific genetic markers were monitored by using real-time polymerase chain reaction (PCR) assays with specific primer sets. Each host-specific genetic marker showed similar responses in non-filtered river water and seawater: They persisted longer at lower temperatures and higher salinities. In addition, these markers did not increase in all conditions tested. Decay rates for indicator organisms were lower than those for host-specific genetic markers at temperature above 10 degrees C. Furthermore, we investigated whether the PCR-detectable 16S rRNA genetic markers reflect the presence of live target cells or dead target cells in environmental waters. The result revealed that the detection of the Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters mainly reflected the presence of 'viable but non-culturable' Bacteroides-Prevotella cells. These findings indicate that seasonal and geographical variations in persistence of these host-specific Bacteroides-Prevotella 16S rRNA genetic markers must be considered when we use them as alternative fecal indicators in environmental waters.