Thermophilic bacteria have been isolated and detected using 16S rDNA sequences from thermal springs in various places around the world. However, there is little or no report on known thermophilic bacteria isolated or detected using 16S rDNA sequences from Manyara and Mbeya thermal springs. The objective of this study was to isolate, characterize and identify thermophilic bacteria using the physiological characteristics. A total of 4 isolates were isolated from Mbeya neutral thermal springs and isolate Many1 was isolated from Manyara alkaline thermal spring. These isolates were rod shaped. The lowest growth temperature for these isolates was 45 oC and the highest 81 oC. The 16S rDNA sequence analysis of 3 isolates showed that they are members of the genus Caldaterra and1 isolate belong the genus Thermus. The results of this study are useful to scientific community and Tanzania as a country should ensure these hot springs are well conserved for research purpose and tourism.