Henneguya sp. myxospores were isolated from the gills of a channel catfish Ictalurus punctatus from a catfish production pond in Mississippi, USA. Plasmodia lacked a defined capsule as seen with other Henneguya spp. associated with catfish aquaculture. Myxospores were morphologically and histologically consistent with Henneguya postexilis; 42.7–49.1 (45.9 µm) in total length, with caudal processes 25.7–38.1 (31.2 µm) long. Spore bodies were 12.1–17.2 (15.5 µm) long, 3.6–4.8 (4.1 µm) wide, and 2.9–3.8 (3.5 µm) thick. Polar capsules were unequal in length, with the longer polar capsules 4.4–6.7 (5.9 µm) long while the shorter polar capsules were 4.4–6.4 (5.6 µm). Polar capsules were 1.1–1.6 (1.4 µm) wide, with each containing coiled polar filaments with 6–8 turns. Histological examination of infected tissues revealed severe lamellar hemorrhage and congestion surrounding the plasmodia. Although H. postexilis has not been previously implicated as a disease agent in catfish production ponds, the original description of the species noted marked pathological changes in the gill structure, consistent with current findings. Molecular data comprised of 2,024 bp of 18S ribosomal RNA (18S), 2,431 bp of 28S ribosomal RNA (28S), and 623 bp of elongation factor 2 (EF2). The morphological and molecular data provided from myxospores will aid in the future identification of H. postexilis. Further, the molecular sequence data will assist in life cycle studies by facilitating linkage of myxospores to the actinospore stage as they are encountered. Additionally, novel 28S and EF2 data are provided from archived myxozoan species using primers developed from draft genomes from other catfish infecting Henneguya spp. These 18S, 28S, and EF2 data were used in concatenated phylogenetic analyses and phylogenetic signal assessments to assess the relative utilities of these markers for phylogenetic inference of myxobolid species. Signal assessment on a concatenated phylogeny including all three regions indicated 18S, 28S, and EF2 contributed 34–50 (47%), 40–51 (41%), and 6–20 (12%), respectively, of phylogenetic signal. While 18S data are commonly provided in accounts of myxobolids, these data suggest that 28S and EF2 may be underutilized in resolving phylogenies of these parasites and could serve as more resolute confirmatory diagnostic markers. This work identifies yet another unique Henneguya sp. from farm-raised catfish and further expands our knowledge of the genetic diversity of myxozoan communities associated with catfish aquaculture in the southeastern United States.