An appeals court ruled yesterday that merging Bronx Criminal and Supreme courts in 2004 was unconstitutional, a decision that prosecutors fear will cause “chaos.”

The Appellate Division said then-Bronx Chief Judge Judith Kaye had no legal standing to merge the courts, which allowed Supreme Court judges to preside over some misdemeanor cases.

Bronx prosecutors said the ruling could throw thousands of misdemeanor convictions into doubt.

The ruling likely will lead to “chaos,” according to a statement from Bronx DA Robert Johnson.