No, molecules are not always equal in a chemical equation. A chemical equation represents a chemical reaction, in which the starting materials (reactants) are transformed into different substances (products). The law of conservation of mass states that the total mass of the reactants must be equal to the total mass of the products. However, the number of molecules of each substance may change during the reaction.

For example, consider the following chemical equation:

$2H_2 + O_2 \rightarrow 2H_2O$

In this equation, two molecules of hydrogen gas ($H_2$) react with one molecule of oxygen gas ($O_2$) to produce two molecules of water ($H_2O$). The number of hydrogen atoms is conserved, as there are four hydrogen atoms on both sides of the equation. The number of oxygen atoms is also conserved, as there are two oxygen atoms on both sides of the equation. However, the number of molecules is not conserved, as there are three molecules on the left side of the equation and two molecules on the right side of the equation.

In general, the number of molecules of each substance in a chemical equation may change during the reaction, but the total mass of the reactants must be equal to the total mass of the products.