The Paradox Basin is a northwest-southeast trending intracratonic basin that formed in southwestern Colorado, southeastern Utah and adjacent parts of Arizona and New Mexico during the late Paleozoic Era. During rise of the adjacent Uncompahgre Uplift (Ancestral Rocky Mountains), the rapidly subsiding basin was filled with over 2000 m of Permo-Pennsylvanian sediments that reflect a complex interplay of changing tectonic, paleoecological, and climatic conditions that resulted in cyclic packages of mixed lowstand and non-marine siliciclastics and highstand shallow-platform carbonates. The 150 m-thick Honaker Trail formation straddles the transition from mostly marine carbonates to mostly non-marine siliciclastics on the southwest shelf of the Paradox Basin during late Moscovian to early Gzhelian (late Desmoinesian to early Virgilian) time. The carbonate-dominated lower 70 m of the formation were divided into two 4th-order sequences and thirteen 5th-order cycles by Goldhammer et al. (1991). We subdivide the remaining overlying 80 m of the Honaker Trail Formation, up to the top of the Shafer Limestone into an additional five 4th-order sequences named, from lowest to highest, the Raplee Limestone (named herein as a replacement for "unnamed limestone" of previous literature), Little Loop Limestone, W"“130 Limestone, Mendenhall Sandstone, and Shafer Limestone sequences and provide a detailed sequence stratigraphic framework of the Raplee, Little Loop, and W-130 sequences. In addition, we provide a conodont sequence biostratigraphic framework for the southwestern (carbonate) shelf of the Paradox Basin to correlate these sequences to Midcontinent (eastern Kansas) cycles using Idiognathodus and Streptognathodus-dominated conodont faunas. From the conodont fauna described herein, the Raplee Limestone sequence likely correlates with the Dennis major cycle of the Midcontinent, and suggests a correlation between the Little Loop Sequence and the minor Hogshooter cyclothem. We also propose the extension of these species' biostratigraphic zones within the Paradox Basin: I. swadei, I. papulatus, I. eccentricus, and I. sulciferus; all of which have been defined by Barrick and Rosscoe (2013) and others as extinct in the Midcontinent Basin at the end of the Swope cyclothem.