Emerging phonological awareness was compared in two groups of 3.5-year-old children belonging to the Jyvaskyla Longitudinal Study of Dyslexia (JLD): children with familial risk of dyslexia (at-risk group n = 98) and children without such risk (control group n = 91). Four computer animated tasks were used: Word-level and Syllable-level Segment Identification, Synthesis, and Continuation of Phonological Units. The control group children manifested higher mastery than children in the at-risk group in phonological awareness, and the proportion of children with a low phonological awareness mean score was 2.5 times higher in the at-risk group than in the control group. In both groups, phonological awareness at 3.5 years was predicted by early language skills assessed between 14 and 26 months of age, and it was also associated with concurrent language. The difference between the at-risk and control group at 3.5-year in phonological awareness remained significant, even when the effect of other language skills such as productive and receptive vocabulary, and mastery of inflections, measured both at earlier ages and concurrently were controlled for. Our findings indicate that familial risk for dyslexia is reliably reflected in emerging phonological awareness already at this early age and it can be assessed independently of other language skills. (Contains 4 tables.)