The quest to understand the relationship between an organism's DNA sequence and three-dimensional form is an interdisciplinary task, integrating diverse fields of the life sciences. The relevance of the metaphor of a genotype-phenotype map is explored from a developmental perspective, in light of the recent concept of a "molecular toolkit" of protein-coding genes, and the widespread view that analyzing the logic and mechanics of gene regulation at multiple levels is key to explaining how morphology is genetically encoded. We discuss the challenges of decoding genomes despite variable genetic backgrounds, the dynamically changing physical and molecular contexts of the internal environment during development, and the impact of external forces on morphogenesis.