Haynes married Bertha Lanterman in October 1887 after a ten-year relationship. The ceremony was held at her parents' Portland home and the couple honeymooned in Cincinnati. Their first child, Marie, was born on January 28, 1889, but she soon succumbed to illness and died when six months old. Their second child, a son born in 1890, also died in infancy. The deaths saddened the family and caused them to turn more to their religion. Haynes became increasingly active in the Presbyterian church and became an elder. In December 1892, the Haynes' third child, Bernice, was born. A second son, March, was born 1896. The two children were well educated and grew up to assist their father in his enterprises.