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DNA-based characterisation of microbial communities can enable those interested in bone diagenesis to address questions relating to the complexity and diversity of said microbial communities. We explored whether biases could be introduced due to differences in the DNA extraction methods used. We investigated the effect of four alternative approaches on the extraction of DNA from bone, in order to examine the resulting effect on the bacterial and fungal OTUs recovered using metabarcoding. We found that the different extraction methods resulted in differences in the microbial OTU profiles generated, both when looking at the fungal and the bacterial communities within the bone. Our results emphasise the need for consistency when working with DNA extraction if comparison of results between different research groups are to be valid. Furthermore, it is clear that future efforts will be needed to determine which methods may provide the most accurate representation of the microbial community in bones.