Offspring of parents with bipolar disorder (BD) or major depressive disorder (MDD) are at high biological risk (HR) of these disorders given their significant heritability. Thus, studying neural correlates in youths at HR-MDD and HR-BD appears essential to understand the development of mood disorders before their onset. Resting-state amplitudes of low-frequency fluctuations (ALFF) and fractioned ALFF (fALFF) shows moderate to high test-retest reliability which makes it a great tool to identify biomarkers. However, this avenue is still largely unexplored. Using the Healthy Brain Network biobank, we identified 150 children and adolescents HR-MDD, 50 HR-BD and 150 not at risk of any psychiatric disorder (i.e., the control group). We then examined differences in relative ALFF/fALFF signals during resting-state. At a corrected threshold, participants HR-MDD displayed lower resting-state ALFF signals in the dorsal caudate nucleus compared to the control group. The HR-BD group showed increased fALFF values in the primary motor cortex compared to the control group. Therefore, robust differences were noted in regions that could be linked to important symptoms of mood disorders, namely psychomotor retardation, and agitation. At an uncorrected threshold, differences were noted in the central opercular cortex and the cerebellar. The database is a community-referred cohort and heterogeneous in terms of children's psychiatric diagnosis and symptomatology, which may have altered the results. ALFF and fALFF results for the comparison between both HR groups and the control group overlapped, suggesting good convergence. More studies measuring ALFF/fALFF in HR are needed to replicate these results.