Humankind depends on plants to harvest solar energy and convert it into accessible chemical energy. With booming human population growth and diminishing availability of arable land, understanding plant development is necessary for more efficient agricultural production. Auxin is a plant hormone utilized in many aspects of plant growth and environmental responses. This work examines genes that regulate or are regulated by auxin, biogenesis and function of an organelle that is an auxin source, and molecules that behave as auxins to influence plant development. Within the plant cell, peroxisomes are organelles that house many processes including fatty acid metabolism to produce energy and also proto-auxin metabolism to produce the active hormone. Peroxisomal proteins are translated in the cytoplasm and imported into peroxisomes by a host of machinery. Peroxisomal targeting signal sequences are recognized by one of two receptors; these receptors interact with each other physically and functionally in some organisms. Here, I identify the receptor machinery present in diverse organisms to predict and compare methods of peroxisomal matrix protein import. I also characterize mutants of the model plant Arabidopsis thaliana defective in import of one class of peroxisomal matrix proteins. In addition, I examine various molecules that influence plant development in an auxin-like fashion. I identify genes with mRNA accumulation regulated by a proto-auxin in a background that inefficiently converts this compound into auxin. I describe the characterization of responses to a second auxin-related molecule that impacts plant development through auxin signaling. I also describe the isolation, characterization, and cloning of a mutant with reduced sensitivity to a specific subset of auxin-like molecules. Data obtained in this work reveal a host of factors that affect auxin regulation and thereby influence plant life. The results of these experiments in plant biology highlight the diversity, complexity, and essentiality of auxin responses.