Animal microbiomes are an integral component of animal fitness and evolution, yet frameworks for understanding how microbial symbiont communities are assembled under natural conditions are yet nascent. In this project, we conceptualize microbiome assembly as a series of ecological filters operating at the environment, host, and host tissue levels, including previously unknown cross-domain interactions between microbial and metazoan symbionts. We are using field surveys across broad geographic scales and field experiments to identify key processes in crayfish microbiome assembly. We are using a combination of DNA fingerprinting and high throughput direct sequencing to characterize the microbiome of a stream inhabiting crayfish (Cambarus sciotensis) and identify key processes at each level. This work is the first exploration of the crayfish microbiome and has already uncovered commonality in symbiotic microbial taxa with the microbiomes of aquatic vertebrates and has shown that very different ecological processes operate at multiple scales to create microbial mosaics on the host body. Our work demonstrates that multi-scale studies of symbiont community assembly provide a more complete picture of how the animal holobiont is assembled under conditions of natural complexity and help identify functionally significant symbiont taxa.