Biodiversity loss is one of the biggest environmental issues in the world today and the biodiversity literacy of citizens can be key to counteracting this. Considering that children can be change agents and actively take part in decision-making from early years, we have assessed the native fauna identification skills of Primary School students (aged 6-12 years-old; n = 1975) from northern Spain along with their conservation preferences regarding common and threatened species. We have observed that, despite students' species literacy increasing with the education level, it remains overall very low. Besides, the conservation preferences of children are not exclusively guided by conservation priorities and, although are partially explained by species identification accuracy, other factors also seem to skew these preferences. These findings point out the need to properly address knowledge of local fauna from the early school years and the urgent need to provide children with the appropriate training regarding the characteristics to be taken into account when selecting species for protection and ensure their conservation.