The growth of bismuth on Ge(001) has been studied using scanning tunneling microscopy. Deposition of one-monolayer (ML) Bi at room temperature and subsequent annealing at 500 K results in the formation of a well-ordered (2 × n) vacancy line network oriented perpendicular to the dimer rows. Deposition of two-monolayer Bi under the same conditions results in the formation of square-shaped pits with depths up to 10 ML. The edges of these pits run along the two dimer row directions. Careful analysis of these pits reveal that they mainly consist of (111) and (113) facets. We argue that the morphological transition from the vacancy line network to the square shaped pits pattern is driven by a modification of the surface strain tensor.