In order to more economically process cellulosic feedstocks using a biochemical pathway for fuel production, it is necessary to develop a detailed understanding of plant cell wall characteristics, pretreatment reaction chemistry, and their complex interactions. However given the large number of thermochemical pretreatment methods that are currently being researched and the extreme diversity of plant cell wall structure and composition, this prospect is extremely challenging. Here we present the current state of research at the interface between plant biology and pretreatment chemistry. The first two sections discuss the chemistry of the secondary plant cell wall and how different pretreatment methods alter the overall cell wall structure. The third section addresses how the characteristics of the cell wall and pretreatment efficacy are impacted by different factors such as plant maturity, classification, and plant fraction. The fourth section summarizes current directions in the development of novel plant materials for improved biochemical conversion. And the final section discusses the use of chemical pretreatments as a screening and analysis tool for rapid identification of amenable plant materials, and for expansion of the fundamental understanding of plant cell walls.