To detect genetic defects that might have caused loss of flagella in Shigella boydii and Shigella sonnei, the region III flagellar (fli) operons were cloned from certain strains and analyzed with reference to the restriction maps and genetic maps of Escherichia coli fli operons. S. boydii NCTC9733 (strain C5 in this paper) had the 988-bp internal deletion in the fliF gene that encodes a large substructural protein of the basal body. Two strains (C1 and C8) had deletions of the entire fliF operon, and the remaining three (C3, C4, and C9) differed in the size of the restriction fragments carrying the fliF and fliL operons. Loss of flagella in S. boydii appears to originate in some defect in the fliF operon. S. sonnei IID969 lacked the fliD gene and, in place of it, carried two IS600 elements as inverted repeats. Genes downstream from fliD were not detected in the cloned fragment despite its large size but did appear elsewhere in the chromosome. The fliD gene encodes a cap protein of the flagellar filament, and its deletion results in overexpression of class 3 operons by the increased amount of FliA ( F ) caused by the excess export of the anti-sigma factor FlgM. Three other strains also had the fliD deletion, and two of them had another deletion in the fliF-fliG-fliH region. The fliD deletion might be the primary cause of loss of flagella in S. sonnei. The lack of FliF or FliD in each subgroup is discussed in connection with the maintenance of virulence and bacterial growth. We also discuss the process of loss of flagella in relation to transposition of IS elements and alterations of the noncoding region, which were found to be common to at least three subgroups.The genus Shigella is divided into four subgroups or species: Shigella dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei (46). All are pathogens which cause diarrhea and dysentery in humans and certain other primates (37). Shigellae have been regarded as nonmotile organisms lacking flagella (15), and this characteristic has been used as one of the taxonomic and diagnostic criteria to distinguish shigellae from other enteric bacteria. However, it has been reported that some prototypical strains of the four subgroups and two fresh clinical isolates of S. sonnei are sparsely flagellate (19). We have not yet detected any motile strain among the four subgroups in the more than 20 laboratory strains we have examined so far; instead we have detected defective flagellar genes in some strains of these subgroups (4, 56). Therefore, we have been studying loss of motility by shigellae from the point of view that almost all shigellae are nonmotile because of a lack of flagellation.Approximately 50 genes, composing at least 13 operons, are involved in the biogenesis and functioning of a flagellum of Escherichia coli and Salmonella typhimurium (33). These operons are clustered into three different regions on the chromosome. Region I operons mainly contain flagellar structural genes designated flg; region II contains a mixture of flagellar (flh) and mot...