The self-assembly of two regioisomeric hydrogen-bonding naphthalenes was studied in mixed states in different polarity solvents. The regioisomers co-assemble to form heteromeric rosettes in chloroform. Upon injecting this solution into methylcyclohexane the heteromeric rosettes kinetically form amorphous aggregates, which over time differentiate into thermodynamically stable distinct nanostructures through self-sorting.