Margaret Clay Ferguson (1863–1951) was an American botanist best known for advancing scientific education in the field of botany.

Ferguson became the first female President of the Botanical Society of America in 1929 and began working as a professor of botany and head of the department at Wellesley College in 1930.

Her study on the latter revealed how plant flower color and pattern do not follow Mendelian laws of inheritance.

Ferguson encouraged many women botanists during her time at Wellesley College, where lab work was a major part of her teaching.

In her later years, Ferguson spent time in Florida before moving to San Diego, where she died of a heart attack in 1951.