During the past decade, rotavirus genotype G9 has spread throughout the world, adding to and sometimes supplanting the common genotypes G1-G4. We report evidence of this spread in a population sample within rural Ecuador. A total of 1,656 stool samples were collected from both patients with diarrhea and from asymptomatic residents in 22 remote communities in northwestern Ecuador from August 2003 through February 2006. Rotavirus was detected in 23.4% of case-patients and 3.2% of controls. From these 136 rotavirus-positive samples, a subset of 47 were genotyped; 72% were of genotype G9, and 62% were genotype PG9. As a comparison, 29 rotavirus-positive stool samples were collected from a hospital in Quito during March 2006 and genotyped; 86% were of genotype PG9. Few countries have reported PG9 rotavirus detection rates as high as those of the current study. This growing prevalence may require changes to current vaccination programs to include coverage for this genotype.