Gregarina lutescens n. sp. is described from the alimentary canal of the harlequin ladybird or multicolored Asian lady beetle, Harmonia axyridis (Coleoptera: Coccinellidae) collected from prairie fleabane, Erigeron strigosus, at Peru State College, Peru, Nemaha Co., Nebraska. Our specimens differ from all 11 known species of Gregarina infecting coccinellid beetles worldwide by differences in size and relative shape, color, and association structure. Gregarina lutescens n. sp. is smaller than 7 known species infecting coccinellid beetles but larger than the other 4 known species based on confidence interval exclusion of means. Our specimens are unique among known species of interest in their quince-yellow cytoplasm and precocious but ephemeral serial associations of up to 5 satellites. Nucleotide sequence (18S) phylogenetic analyses place the new species basal to a member of an internal clade of Gregarina that comprises gregarines parasitizing chrysomelid beetles. Phylogenetically, the analysis recovered 3 major lineages within the gregarines, representing the superfamilies Gregarinoidea, Stenophoroidea, and Stylocephaloidea and indicating the propensity of gregarines to track host lineages and environments through evolutionary time. These findings confirm the polyphyletic nature of Gregarina, which currently comprises over 300 described species, only a handful of which have documented genetic sequences suitable for phylogenetic analysis. Recollection, redescription, and molecular clarification of gregarine species infecting coccinellids would likely result in identification of a unique clade that would be an excellent system for studying the effect of intraguild host competition on parasite diversification and community structure. Ecologically, patterns of prevalence in this study indicate that G. lutescens reproduces primarily in larval hosts but depends on infections in adult beetles to overwinter, reflecting the differential vagility and frost tolerance of larval and adult host life cycle stages.