Sexual dimorphism is characteristic of monogonont rotifers, but at present, most investigations on the evolution of morphology within Monogononta have focused exclusively on females, with only minor taxonomic comments on the male structure. Here, we make the first detailed comparison of female and male morphology by examining their muscular organization, with the aim of understanding how factors such as phylogeny, habitat and the structural rigidity of the body wall determine the muscle arrangement patterns. We compare the musculature of both females and males in Brachionus manjavacas and Epiphanes senta. Generally, rotifer males have a similar ecology that may be different from the conspecific females. Thus, we analysed muscles of conspecific females and males with different ecology, namely habitat and/or different stiffness of the lorica. Females of B. manjavacas are loricate and planktic, while E. senta females are illoricate, can be found in the plankton, but have a lifestyle much related to a substrate. Males are in both species free swimmers and without a stiff lorica. Visceral muscles are present in the digestive (only in females) and reproductive apparatus (only in males). Somatic musculature comprises inner longitudinal and outer circular muscles. Major differences are discernible among circular muscle states: B. manjavacas has dorsoventral bands, while E. senta possesses muscles that are ventrally incomplete. The same condition occurs in both sexes. Results from analyses on female rotifers support that the circular arrangement is a variable trait that mainly reflects morpho-ecological adaptations, potentially related to the development of a lorica. The presence of an identical condition in the conspecific males, independently of their ecology, suggests, however, that this variability may be limited by evolutionary and developmental constraints. Further investigations should be required to clarify whether males have different arrangements from their females, and thus whether their musculature may be informative for phylogeny within monogononts.