Molecular equations are chemical equations that show the reactions of compounds, whether ionic or covalent, only as compounds and not as dissociated ions. It is only a meaningful distinction for reactions involving ionic compounds since covalent compounds do not have dissociated ions. The other type of equation is an ionic equation, which shows the dissociated ions with their respective charges.
Molecular equations are relatively simple to write, but they also often misrepresent the reactions they symbolize. This is because these reactions often occur in aqueous solutions, where only some of the components actually react. For instance, a molecular equation of calcium chloride and silver nitrate shows the creation of calcium nitrate and silver chloride. This is misrepresentative in two ways. First, the actual available reactants are not calcium chloride and silver nitrate but fully dissociated calcium, chloride, silver and nitrate ions. Further, the only compound actually created is silver chloride, which is an ionic solid that precipitates out of the solution. The other ions, calcium and nitrate, do not react and stay in solution. An ionic equation can be simplified to remove these nonreacting components entirely.
The molecular formula can be valid and useful as a conceptual aid, or it can serve as a more accurate model if the water is removed after the reaction by boiling or some other method that leaves the dissolved ions behind to associate into ionic compounds.