The graduate program in botany emphasizes systematics and the evolution of higher plants. Sub-disciplines include monographic and revisionary studies, population and conservation genetics, molecular systematics, phylogenetics, plant anatomy, floristics, comparative morphology, biogeography and reproductive biology. Thesis work leading to the Master of Science (M.S.) or Doctor of Philosophy (Ph.D.) degree may be carried out in any of these fields. The program is research intensive with a strong fieldwork component.

The CGU Department of Botany is unique in that it is located within one of Southern California's premier gardens—California Botanic Garden—86 acres dedicated to the conservation of the state's flora, to the display of native plants for visitors and to research and graduate education. Graduate classes and laboratories, faculty and student offices, and all research facilities used by students are located at CalBG, in close proximity to the CGU campus. The program benefits from The Claremont Colleges, through which botany graduate students may take courses at any of the undergraduate Claremont Colleges or from any of the other graduate programs that are part of CGU. Additionally, a seminar series addressing topics of systematic and evolutionary botany is offered routinely during each semester. This series draws attendees not only from our student body, but also from plant science researchers, faculty and students at nearby colleges and universities.

The botany program cultivates a collegial, interactive atmosphere in which graduate students participate as colleagues with faculty in the common pursuit of excellence in scholarship and research. Graduate students are expected to be independent, self-motivated, and enthusiastic about learning and about undertaking and completing original research. Because of these expectations and our commitment to maintaining an atmosphere that promotes research productivity, prospective graduate students are carefully screened to ensure high academic standards and compatibility with the ethos of the botany program. Therefore, the objective guidelines below may be less important in individual cases than demonstrated research ability or intellectual independence.

The CGU Department of Botany at CalBG prepares its graduates to compete with top-caliber graduates in the field. The graduate student population is small, usually 10–15, and competition for existing positions is keen. Requirements for admission are rigorous and prospective students must have a strong academic record, excellent references and demonstrate a commitment to botanical research. Prospective students are encouraged to study admission requirements and to contact faculty whose research interests parallel their own.

Students in the Botany Program receive tuition waivers from CGU except under unusual circumstances. Full-time students are also eligible to apply for additional financial aid in the form of research and teaching assistantships. Research assistants work with CalBG faculty on a specific project over the course of a semester. Teaching assistants are apprenticed to one of the graduate courses and usually have responsibility for laboratory exercises. There are also teaching assistantships available in areas outside the graduate program such as community education. Students in good standing are also eligible for research support in the form of small grants. These are intended to enable students to launch their research projects and to collect the preliminary data required to successfully compete for funding from outside sources.

Programs of study and research leading to both master's and doctoral degrees are offered. Master's students normally have 2.5 years (5 semesters) to complete and defend the thesis; Ph.D. students are expected to complete their degrees within five years.