who's eyes were watching God?

The meaning of the title isn't directly dealt with in any detail. Still there are clues through the book. There are two quotes that allude to the title,

"The time was past for asking the white folks what to look for through that door. Six eyes were questioning God"....." Shortly thereafter, a second important sentence appears: "They seemed to be staring at the dark, but their eyes were watching God."

Both quotes are connected to the theme of race. There is the sense of blacks looking to God when the answers are not revealed or unsatisfactory by white people.