Calcite-forming by bacteria has been reported in various geological environments including limestone caves, and soil. There are four natural processes by which calcite is formed: carbonic anhydrase (CA), sulphate reduction, nitrate reduction, and urea hydrolysis. The aim of study is to identify calcite-forming bacteria occurring in limestone areas of Malaysia. Ten bacilli were identified to capable of calcite forming out of 23 total isolates. The processes of calcite forming were found to be either CA or urea hydrolysis, as none of the isolates falls into nitrate or sulphate reducing type of calcite-forming bacteria. Identification using 16S ribosomal DNA gene sequencing with polymerase chain reaction (PCR) identified B.sphaericus, B.cereus and B. pumilus; B.sphaericus, and B.cereus falls into urea hydrolysis and CA type, whereas B.pumilus falls into CA type of calcite forming.