Tomitaro pursued botanical studies in earnest and went to Tokyo with aspirations in 1884 again. He was allowed to use books and specimens in the botany classes at the Faculty of Science of Tokyo University and devoted himself to plant studies there. In those days, Japanese researchers sent plants abroad to have them identified. Tomitaro sent some to Maximowicz, a Russian authority on plant studies in East Asia. Tomitaro was a gifted artist, as confirmed by the letter Maximowicz sent back to him highly praising his drawings.

While Tomitaro was very active in pursuits such as the issue of Nihon Shokubutsushi Zuhen (Illustrated Flora of Japan) and the definition of a series of new species, his family's business began to decline as he spent too much money for his study. He also fell out with Ryokichi Yatabe, a professor in the Botany Department. In 1891 he went home in Sakawa to dispose of property. He was working hard on sketching and collecting plants in Kochi when he was invited to the Imperial University's College of Science in Tokyo to act as an assistant by Jinzo Matsumura who had become a professor in the Botany Department.

After having a family and a child, he worked as a university assistant in the Botany Department. However, his family budget became tight and the relationship with Prof Matsumura was not going well. In this extremely difficult situation, Dainihon Botanical History was published, containing the most exquisite botanical illustrations. He was also invited to teach at local plant collecting societies and started his own club to teach. Underlying his never giving up on plant research, no matter what the circumstances, was his own deep love for plants and the great support of his family and other acquaintances.

In 1926, he settled in Oizumi Village, Kita Toshima County (current location of Makino Memorial Garden), where he lived until his death. In 1927, Tomitaro received a Doctor of Science, but he regretted it later because he felt as if he had become ordinary. The following year, his wife Sue, who had been devoted to Tomitaro, passed away. As a token of his gratitude, Tomitaro decided to give his wife's name to Sasa (some sort of bamboo), which he had just discovered in Sendai, and named it Suekozasa. Overcoming his sadness, Tomitaro continued to travel to different parts of the country to collect plants. Meanwhile, he started editing a botanical illustrated book, which was finally completed after nearly ten years and published it in 1940. He resigned from the university in 1939, where he had worked as a lecturer for 47 years. He also devoted himself to writing to spread knowledge of plants, publishing botanical essays.