Ben Howard explained the song's meaning to The Sun: "'Black Flies' is about someone I don't really speak to anymore. It's an observational song about the changes in the year. It's not about romance as a few people have suggested."
Howard explained to Reuters that the song is a tale of a ruined friendship. "We ended up doing separate things and going separate ways," said the singer. "That's what I write about most of the time, the people who come in and out of our lives and the memories that you form around them."