Extracellular DNA, attributed to dead or dying organisms, is known to be significant component of shallow marine sediment. The prevalence of extracellular DNA in sediment deeper than 10cm below the seafloor and the degree to which extracellular DNA signatures may skew surveys of microbial life in this habitat had remained untested. To address these pertinent questions, I embarked on two oceanographic expeditions to the Mid-Arctic and Eastern Pacific ocean and collected fresh subseafloor sediment samples amenable to intra- vs. extra-cellular DNA interrogation using the DNA-binding photoactive dye propidium monoazide. Photoactive dye-treated samples allow the amplification and subsequent high-throughput sequencing of intracellular DNA, exclusively. Thus, comparisons to untreated controls, where both extra- and intra-cellular signals are amplified and sequenced, show the influence of the environmental extracellular DNA component in gene quantification and community sequencing surveys. Significantly higher 16S rRNA gene counts from total versus intracellular DNA pools in shallow sediment confirm the presence of extracellular DNA pools in shallow marine sediment. All samples collected from depths greater than 10 cm did not show differences in 16S rRNA genes quantified from total vs. intracellular DNA pools. 16S rRNA gene sequencing shows that even where there are significant differences in intracellular vs. total (intra- and extra-cellular) gene counts, the reported microbial community composition remains the same. Overall, we show that despite its intermittent detection in shallow sediment, extracellular DNA is not detected and does not affect 16S rRNA gene-targeted community composition surveys in sediment as deep as 10 meters below the seafloor.