During the Civil War, on the ninth of March in 1937, he married Josefina Manresa Marhuenda, whom he had met in 1933 in Orihuela. His wife inspired him to write most of his romantic work. Their first son, Manuel Ramón, was born on 19 December 1937 but died in infancy on 19 October 1938. Months later came their second son, Manuel Miguel (4 January 1939 – 1984). Josefina died on 18 February 1987 at age 71 in Elche, Alicante.

Unlike others, he could not escape Spain after the Republican surrender and was arrested multiple times after the war for his anti-fascist sympathies, and was eventually sentenced to death. His death sentence, however, was commuted to a prison term of 30 years, leading to incarceration in multiple jails under extraordinarily harsh conditions until he eventually succumbed to tuberculosis in 1942. Just before his death, Hernández scrawled his last verse on the wall of the hospital: Goodbye, brothers, comrades, friends: let me take my leave of the sun and the fields. Some of his verses were kept by his jailers.

In July 2010 the poet’s family filed a lawsuit in the Spanish Supreme Court in which they asked for his guilty verdict (for his supposed crime of left wing sympathies), to be annulled. In 1939 he had been condemned to death as “an extremely dangerous and despicable element to all good Spaniards.” Franco later reduced the sentence so that he would not become an international martyr, as Lorca did. In March 2010 the family had a posthumous “declaration of reparation” from the Spanish government, but, his daughter-in-law Lucía Izquierdo said: “We want something more, that they void the death sentence.. that they hand down a ruling of innocent”. Lawyers for the poet’s family had new evidence, a 1939 letter from a fascist military official, Juan Bellod, testifying to his innocence. “I have known Miguel Hernández since he was a boy”, the letter began. “He is a person with an impeccable past, generous sentiments and deep religious and humanist training, but whose excessive sensitivity and poetic temperament have led him to act in accordance with the passion of the moment rather than calm, firm will. I fully guarantee his behaviour and his patriotic and religious fervour. I do not believe that he is, at heart, an enemy of our Glorious Movement”.