Adolescence is a particularly important time for the development of self-perceptions and identity as many environmental and personal factors are influential. One relatively unexplored factor is level of motor competence. To examine the relationship between identity health and self-perceptions in male and female adolescents with low motor competence (LMC) compared to typically developing (TD) adolescents. Adolescents (N=160, 64.4% males, Mage=14.45yrs., SD=0.75) completed the Adolescent Motor Competence Questionnaire (AMCQ), Assessment of Identity Development in Adolescence (AIDA), and Harter's Self-Perception Profile for Adolescents (SPPA). Based on the AMCQ score, the sample was grouped into LMC and TD. Pearson's product moment correlations between the AIDA and SPPA subscales were derived for gender, competence groups, and gender x competence sub-groups. Overall, males had lower AIDA scores (healthier identity) than the females and significant associations with all self-perception domains. For females, only scholastic and social competence, physical appearance, behavioural conduct, close friendship and Global Self-worth (GSW) domains were significantly related to their AIDA score. The adolescents in the LMC group had higher AIDA scores (less-healthier identity) and fewer self-perception domains [scholastic competence, physical appearance, behavioural conduct, close friendships and GSW] were associated to their AIDA scores. For the TD group, all self-perception domains were significantly correlated with their AIDA scores. When grouped by gender and motor competence, the TD males had the healthiest identity scores which were strongly associated with all self-perception subdomains. For males with LMC, only scholastic competence, behavioural conduct and GSW domains were significantly related with their identity score. Females from both competence groups reported significant associations between physical appearance, close friendships, behavioural conduct, and social competence domains with their identity scores. Scholastic competence was also significantly associated with identity only for females with LMC. Positive self-perceptions across a range of domains are associated with a healthier identity, but differ according to level of motor competence and gender. For those with LMC, the self-perception subdomains unrelated to physical activity and sport, such as school-based aspects were associated with a healthier identity. These findings should guide school based interventions to provide support in these domains in order to strengthen self-worth and identity health.