"As this is a private and personal matter, he asks that the public and the media kindly respect the privacy of Kai, his children, and family at this time," read a statement from Wonder.
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The Grammy winner is known for his hits "Superstition," "I Just Called to Say I Love You" and "Signed, Sealed, Delivered I'm Yours."
TMZ said the couple have been separated since October 2009.
The 62-year-old is requesting joint custody of his two sons, Kailand and Mandla, ages 10 and 7, TMZ confirmed.
ABC News reported this is his second marriage. Wonder was previously married to the late singer and songwriter Syreeta Wright.