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Decay experiments are becoming a more widespread tool in evaluating the fidelity of the fossil record. Character interpretations of fossil specimens stand to benefit from an understanding of how decay can result in changes in morphology and, potentially, total character loss. We performed a decay experiment for the Class Enteropneusta to test the validity of anatomical interpretations of the Burgess Shale enteropneust Spartobranchus tenuis and to determine how the preservation of morphological features compares with the sequence of character decay in extant analogues. We used three species of enteropneust (Saccoglossus pusillus, Harrimania planktophilus, and Balanoglossus occidentalis) representing the two major families of Enteropneusta. Comparisons between decay sequences suggest that morphological characters decay in a consistent and predictable manner within Enteropneusta, and do not support the hypothesis of stemward slippage. The gill bars and nuchal skeleton were the most decay resistant, whereas the gill pores and pre-oral ciliary organ were unequivocally the most decay prone. Decay patterns support the identification of the nuchal skeleton, gill bars, esophageal organ, trunk, and proboscis in Spartobranchus tenuis and corroborate a harrimaniid affinity. Bias due to the taphonomic loss of taxonomically informative characters is unlikely. The morphologically simple harrimaniid body plan can be seen, therefore, to be plesiomorphic within the enteropneusts. Discrepancies between the sequence of decay in a laboratory setting and fossil preservation also exist. These discrepancies are highlighted not to discredit the use of modern decay studies but rather to underline their non-actualistic nature. Paleoenvironmental variables besides decay, such as the timeframe between death and early diagenesis as well as postmortem transport, are discussed relative to decay data. These experiments reinforce the strength of a comprehensive understanding of decay sequences as a benchmark against which to describe fossil taxa and understand the conditions leading to fossilization.