Background and aimsA relationship exists between an adolescent’s level of motor competence and the health of their identity. As those with low motor competence (LMC) form less healthy identities, the aim of this study was to investigate if self-perceptions mediated the negative impact of LMC on identity health.MethodsAdolescents (N = 160) completed the Adolescent Motor Competence Questionnaire (AMCQ), Assessment of Identity Development in Adolescence (AIDA) and the Self Perception Profile for Adolescence (SPPA). The mediating effect of their self-perceptions on the relationship between motor competence and identity health was examined in several ways: for the total sample, between male and females, and level of motor competence. Two motor competence groups were formed by dichotomizing their AMCQ scores (< 83 = LMC).ResultsThere was an indirect effect of self-perceptions of social competence, physical appearance, romantic appeal, behavioural conduct, close friendships and global self-worth on the relationship between motor competence and identity health for the total sample (N = 160, 64.4% males, Mage = 14.45 SD = .75, 12 to 16 years). No indirect effects were significant for females however close friendships and global self-worth were significant for the males. When the sample was grouped for motor competence, indirect effects of social competence, athletic competence, physical appearance, behavioural conduct, and global self-worth were significant for the high motor competence (HMC) group. The only self-perception significant for the LMC group was close friendships.ConclusionSelf-perceptions in several domains mediated the relationship between motor competence and identity health, and these differed for level of motor competence but not gender. Those with LMC who had a higher self-perception in the close friendships domain had a healthier identity. Designing physical activity programs that focus on skill development and forming close friendships are important for adolescents with LMC.