Connecting genotypes, the genetic information in an organism, to phenotypes, the functions that an organism performs, is one of the important challenges of biology. In this study, I identified strains of Gammaproteobacteria that are genetically similar, but display varying phenotypic profiles. I investigated the genetic source of the functional variation and gene expression that accounts for their phenotypic differences. Bacteria were isolated from both the water column and surface/tissue of kelp species Macrocystis pyrifera from three locations off the coast of southern California (Catalina Island, La Jolla, and Point Loma). Isolated strains were sequenced using various Next Generation Sequencing platforms, their sequences were assembled using SPAdes and MIRA, and assembled sequences were then annotated using Rapid Annotation using Subsystem Technology (RAST). Phylogenetic association was formulated using five highly conserved housekeeping genes (ftsZ, gyrB, mreB, recA, rpoA) in order to increase sensitivity. Isolate phenotypes were tested using multi-phenotype assay plates, and resulting growth curves analyzed using the high-throughput analysis pipeline PMAnalyzer to create phenotypic profiles. Phenotypic profiles were then compared to phylogenetic analysis to identify genetically similar, but phenotypically varying isolates. Two strains were chosen for this work, ED144 and ED252. Further genetic analysis was performed using various bioinformatics tools to analyze individual strain structure, metabolism, and functional subsystems in order to identify the cause of phenotypic variation. Flux-balance analysis (FBA) successfully identified the genes associated varied biomass production on select media of interest. For conditions where both strains grew but there was a difference in growth, FBA successfully predicted the comparative biomass for four of the media tested, but predictions conflicted with growth results with three of the media tested. For the successfully predicted biomass comparisons, differences in predicted growth involved varying flux in reactions common to both isolates, as well as unique reaction expression in ED252. Identification of the basis of phenotypic and genetic variation can lead to further understanding of their source within the environment, how variation affects cell survival, and whether variation is ecologically significant to kelp health. This work has helped improve genome annotation for future microbiologists.