Chronic wounds are a significant public health burden and associated with complex polymicrobial communities. Bacterial colonization has been hypothesized to be one of the main underlying causes of chronic wounds and leads to detrimental effects on wound healing. However, some members of the wound microbiota may also have beneficial effects on wound healing. The wound microbiome has been underappreciated because of the limitations of standard microbiological culture techniques. The aim of this study was to characterise the bacterial population in healing versus non-healing wounds and to identify possible biomarkers to predict wound healing trajectory by using culture independent next-generation sequencing. Wound swabs were sampled from 18 healing wounds and 30 non-healing wounds. High-throughput pyrosequencing with barcoded primers targeting the 16SrDNA gene was used to generate organism specific sequences. Sequence analysis and data mining was performed using QIIME and Calypso software programs. Principle Component Analysis revealed that there is a distinct difference in the microbial population associated with the healing vs non-healing wounds. Furthermore, OTUs (Operational Taxonomical Units) and taxonomic assignments identified 185 genera in both wound categories. Abundances of some bacterial genera/species were significant (p<0.05) in healing wounds and visa versa. These species can be considered as biomarkers for healing and non-healing wounds. In addition, this study suggests that the high abundance of species in non-healing wounds can be used to improve chronic wound management.