Captain Stefan King, an Iraq veteran and commanding officer of HMAS Albatross at Nowra, is accused of having several love affairs while falsely claiming entitlements for being stationed away from his wife.

The prosecution argues Captain King had emotionally and sexually separated from his wife and was not entitled to the money.

But his former wife, fellow navy Captain Jacqueline King, told a court martial in Canberra on Monday her former husband continued calling their Jerrabomberra house his home while they were separated.

And, she said, they continued to jointly pay the mortgage and share financial commitments tied to their shared lives.

Captain Stefan King is pleading not guilty to 19 charges of fraudulently claiming about $38,000 in allowances to which he was not entitled because he was allegedly no longer in a proper relationship with his wife.

Dozens of pages of emails sent between Captain King and his former lover, dating back to 2008, have been tendered to the court.

But Captain Jacqueline King told the hearing she believed her ex-husband was not the type of officer who would take ''one dollar'' to which he was not entitled. ''Absolutely not; it's not in his DNA,'' she said.

The case will rest on whether the couple remained married, but technically separated, while they continued to live together at the Jerrabomberra house for more than a year before their divorce, as the defence has argued.

If their marriage had collapsed, as the prosecution argued, then Captain Stefan King claiming allowances available to married couples separated by navy work would have been fraudulent.

Captain King became eligible for the allowances in January 2010, the court has heard, but on April 28 that year the couple had a conversation about ending their marriage.

''He knew I was unhappy,'' Captain Jacqueline King told the court.

''He was unhappy. He felt the unhappiness was such that we should consider no longer continuing our marriage.''

The couple stopped sharing a marital bed that night, she said.

In an affidavit signed on May 17 2011, Captain Stefan King said he had believed the marriage had been over from April 27, 2010.

The prosecution argues he was not eligible for entitlements for this period, and claimed them fraudulently.

But Captain Jacqueline King was adamant that the pair sleeping in separate beds did not mean they were no longer married.

The defence has argued the marriage was over only when the couple's divorce was finalised, and therefore no fraud occurred.

While Captain Stefan King was stationed away from homehe continued to come home on weekends, the court heard.

The trial continues.