(U-Th)/He thermochronology is a well-established dating technique used to understand the temperature-time histories of rocks in a wide range of geologic settings. The technique is presently restricted to rocks that contain specific accessory minerals, such as apatite or zircon. Marine carbonates and shales typically lack these accessory phases in quantities and sizes practical for (U-Th)/He dating and thus present a challenge for application of the method. Here, we explore the utility of biogenic apatite from conodonts as a (U-Th)/He thermochronometer at a well-studied calibration site located in eastern Nevada and southwestern Utah.We performed (U-Th)/He thermochronometry, laser ablation inductively coupled plasma mass spectrometry, X-ray micro-computed tomography, and scanning electron microscopy (SEM) on specimens with conodont color alteration indices (CAI) of 1.5–3, extracted from carbonate rocks in the footwalls of low-angle normal faults in the Mormon Mountains, Tule Spring Hills, and Beaver Dam Mountains. Conodont (U-Th)/He (CHe) dates have high scatter; dates are commonly reproducible to 20% of sample means but can deviate up to 150%. All CAI 1.5–2.5 conodonts produce CHe dates younger than 240 Ma, consistent with thermal resetting of samples; however, most CAI 3 conodonts give ages 2–6× older than Mississippian and Permian deposition. Average U, Th, and rare earth element (REE) concentrations depend on porosity and permeability differences between albid and hyaline conodont tissue and range from <10 to 100 s of ppm in concentration. Parent isotope concentrations are especially low in CAI 3 conodonts, commonly <1 ppm, and there is an inverse relationship between these concentrations and CHe dates. The majority of parent U, Th, and Sm and REEs are concentrated within the outer 5 μm of the conodont elements and consistently show 5–10× enrichment relative to cores. Margin enrichment is also depressed with increasing CAI. SEM imaging shows a shift in the orientation of apatite microcrystallites from perpendicular to parallel to the major axes of the conodont elements at CAI 3 and corrosion and recrystallization features, likely associated with burial and diagenesis, on the surfaces of some CAI 2.5 and 3 conodonts.We propose that microstructural changes associated with increasing CAI influence CHe dates. Parent isotope loss occurs during the post-cooling stage, either in the outcrop or in the laboratory. Our hypothesis is that the double-buffered formic acid procedure for dissolving dolomitized carbonates may accelerate this loss in thermally altered, higher CAI conodonts.