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The giant kelp, Macrocystis pyrifera, spans gradients in light, temperature and nutrient availability both within its geographic distribution and the range of depths that individual sporophytes span. M. pyrifera is a member of the brown algae (Phaeophyceae), a complex multicellular group divergent from other eukaryotes; the application of sequence-based tools to study the ecology and evolution of this group is reviewed. To understand the biological response of this ecologically important alga to its environment, it is important to quantify the temporal scales of environmental variation. A several-year thermistor chain time series examined depth-specific variations in temperature and nutrients within a kelp bed. In addition to long-term seasonal changes, rapid vertical variations in the depth of the nutricline were observed, as much as 10m vertical displacement over the span of a few hours. Tools capable of examining the M. pyrifera physiological response on this temporal scale had not yet been developed. Due to the lack of available genomic data for the giant kelp, I utilized next-generation transcriptomic sequencing to increase the number of annotated transcriptional units for this species. M. pyrifera samples collected at different depths enabled transcriptomic exploration of metabolic function across environmental gradients. Depth-dependent transcription patterns were apparent and transcript annotation facilitated the identification of physiological responses to environmental factors. At the surface, where irradiance levels are highest and the potential for oxidative damage is most intense, physiological processes were focused on the capture of light energy for photosynthesis as well as protection from the damaging effects of the sun. M. pyrifera has multiple light harvesting complexes, including some in the LI818 group. Genes involved in nutrient acquisition, genetic information processing and degradation were more highly expressed at depth where colder temperatures and more nutrients occur. This dissertation provides the first transcriptomic characterization of M. pyrifera, develops sequenced-based tools and demonstrates their use to study transcriptional patterns in the context of this alga's natural and variable environment