A culture-independent molecular survey indicates that the composition of bacterial communities is distinctly partitioned between travertine depositional facies in the surface drainage system of Spring AT-1 at Angel Terrace, Mammoth Hot Springs, Yellowstone National Park. PCR (polymerase chain reaction) amplification and sequencing of 16S rRNA genes with universally conserved bacterial primers has identified over 553 unique partial and 104 complete gene sequences (derived from more than 14,000 clones), affiliated with 221 unique species that represent 21 bacterial divisions. These sequences exhibited < 12% similarity in bacterial community composition between each of the travertine depositional facies. This implies that relatively little downstream bacterial transport and colonization took place despite the rapid and continuous flow of spring water from the high-temperature to low-temperature facies. These results suggest that travertine depositional facies, which are independently determined by the physical and chemical conditions of the hot spring drainage system, effectively predict bacterial community composition as well as the morphology and chemistry of travertine precipitation.