Interrogation of gene regulatory circuits in complex organisms requires precise tools for selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed "Biotagging" that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell compartment-specific effector lines, we demonstrate the specificity of the Biotagging toolkit at the biochemical, cellular and transcriptional level. We use Biotagging to characterise the in vivo transcriptional landscape of migratory neural crest and myocardial cells in different cellular compartments (ribosomes; nucleus). These analyses reveal a comprehensive network of coding and non-coding RNAs, and cis-regulatory modules, demonstrating that tissue-specific identity is embedded in the nuclear transcriptomes. By eliminating background inherent to complex embryonic environments, Biotagging allows analyses of molecular interactions at high resolution.