Microorganisms participate in soil carbon storage by contributing biomass in the form of refractory microbial cell components. Despite the important contribution of microbial biomass residues to the stable carbon pool, little is known about how the contribution of these residues to soil carbon storage varies as a function of depth. In this study, we evaluated microbial residue biomarkers (amino sugars) for varied pedogenic horizons from six soil profiles of two geographic sites on a glacial landscape toposequence in Dane County, WI. Our analyses revealed that the amino sugars preferentially accumulated in subsoil. Specially, although the total amino sugar amounts decreased downward through the profile as organic carbon did, the rate of decrease was significantly lower, suggesting that these compounds are more refractory than general soil organic carbon. The proportion of amino sugars to soil organic carbon increased along the depth gradient (from top to bottom), with the exception of Bg horizons associated with high water tables. We also observed that microbial residue patterns measured by amino sugar ratio (e.g., glucosamine to muramic acid) showed different dynamic tendencies in the two different geographic sites, suggesting that residue carbon contribution by fungi and bacteria is likely site-specific and complex. In summary, regardless of redox microenvironment by groundwater dynamic in a given soil, our study supports the idea that microbial residues are refractory and that they contribute to terrestrial carbon sequestration.