The Central Institute of Forensic Science (CIFS) has been providing DNA testing services to Thai people since 2002. Bone accounts for majority of the biological specimens tested, constituting approximately 26% in total evidence. DNA recovery from the bone is challenging owing to degradation and the presence of inhibitors. Therefore, guidelines for bone selection, extraction, and DNA typing are essential for the routine laboratory of CIFS to maximize DNA yield, and minimize time and cost. In this study, we extracted three types of bones: femur, occipital, and petrous, from 12 bodies using a modified organic extraction and silica-based method. The success rate of the Short Tandem Repeat (STR) typing was determined through the number of reportable loci. Furthermore, analysis of mitochondrial DNA (mtDNA) was performed using the massively parallel sequencing technique. Coverage and variant analyses of all samples were evaluated. The results indicate that the femur exhibits the highest success rate in STR typing. The results, in decreasing order, are as follows: femur > petrous > occipital. We determined that silica-based extraction is the most efficient technique for the STR typing; however, modified organic extraction can be used as an alternative method in obtaining mtDNA. The outcome from this study could serve as a guide for identifying human remains and missing persons in the CIFS laboratory, as well as other Thai forensic laboratories.