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Jon H. Shepard was born in Weiser, Idaho in 1941, and spent his high school years in Washington state. Interested in insects, and especially butterflies, from an early age, Shepard enrolled at Oregon State College in 1961, following two years of coursework at a community college. While at Oregon State, Shepard participated in the school's Honors Program, writing an honors thesis - which was later published - on a genus of blue butterflies. As an undergraduate, he likewise conducted bibliographic work on asilid flies in support of Charles Martin, an Oregon State Entomology professor. He completed his Biology degree at OSU in 1963 and earned a master's degree in Entomology from Washington State University in 1965.

Shepard and his wife relocated to Nelson, British Columbia in 1966, a community that served as their home base for more than forty years. During that time, Shepard carved out a career in lepidoptery, teaching at community colleges, serving as a sabbatical replacement for various colleagues, and engaging in contract work. He also pursued his own research and collecting agendas, and in 1974 he began a long tenure as the regional coordinator for the Season Summer Lepidoptera Society.

Over the ensuing decades, Shepard researched butterflies all across the Pacific Northwest. In the early 1990s, he worked with the James Entomological Collection at WSU, and in the late 1990s he joined a group of Northwest lepidopterists known as The Evergreen Aurelians. He also co-authored a book, The Butterflies of British Columbia, that was published in 2001.

Shepard's interests shifted toward moths in the early 2000s, and he spent much of the decade collaborating on the Pacific Northwest Moths Collection, a massive project managed out of Western Washington University. In the summer of 2014, Shepard and his wife moved to Corvallis, where Jon became involved with the Oregon State Arthropod Collection, working as a volunteer curator and donating his own personal collection to the repository.