This study investigated parenting behaviors of mothers and fathers of clinically anxious preschool children (with or without depressive comorbidity) and healthy comparison children. Studies assessing children from early school age onwards have found that parental control, rejection, and inconsistent discipline are associated with the presence of children’s internalizing symptoms/disorders. Despite the scarcity of studies investigating these associations at preschool age, we assumed that findings with older children would also apply to children in this age group. In a cross-sectional study we assessed N = 176 children of preschool age (M = 5; 2 years) and both of their parents. A diagnostic interview (Preschool Age Psychiatric Assessment) was conducted to determine children’s psychiatric diagnoses, yielding the following results: a group of n = 67 children with pure anxiety disorders (AD group), a group of n = 38 children with anxiety disorders with depressive comorbidity (AD/DC group), and a comparison group of n = 71 children without psychiatric disorders. Both parents completed the German extended version of the Alabama Parenting Questionnaire. We evaluated maternal depressive symptoms and children’s temperament as further correlates. All variables that differed significantly between groups were entered into multinomial logistic regression analyses to test which variables predict group membership. When comparing each of the two anxiety groups with the comparison group we obtained the following results: (1) Inconsistent paternal discipline and maternal depressive symptoms increased and children’s positive affectivity decreased the probability of children of being in the AD group rather than in the comparison group. (2) Maternal overinvolvement, maternal depressive symptoms and children’s negative affectivity increased and children’s positive affectivity decreased the probability of children of belonging to the AD/DC group rather than to the comparison group. When comparing the two anxiety groups with each other, we found that inconsistent paternal discipline increased and children’s negative affectivity decreased the probability of children of being in the AD group rather than in the AD/DC group. The results suggest that paternal parenting behaviors show different associations with internalizing disorders at preschool age than maternal parenting behaviors. This underlines the importance of including fathers in the prevention and treatment of internalizing disorders at preschool age.