We report on a simple way to mark and track individual molecules self-assembled on a surface by scanning tunneling microscopy. The tracer mechanism consists in a minimal one-atom chemical substitution. While this substitution leads to significant modifications in the STM signature of the molecules, no substantial changes of the physics of self-assembling are observed when using the modified or unmodified molecular building blocks. This allows us to follow the intrinsic dynamical properties of the self-assembled molecular patterns.