The filing comes days after Heuermann was taken into police custody and charged with the killings of Melissa Barthelemy, 24, Megan Waterman, 22, and Amber Lynn Costello, 27—three women whose remains were discovered in 2010 along a remote highway near Gilgo Beach, N.Y.
On July 14, Heuermann pleaded not guilty to three counts of first-degree murder and three counts of second-degree murder.
"There is nothing about Mr. Heuermann that would suggest that he is involved in these incidents," his defense attorney Michael J. Brown told E! News in a statement. "And while the government has decided to focus on him despite more significant and stronger leads, we are looking forward to defending him in a court of law before a fair and impartial jury of his peers."
Police said in a bail application obtained by E! News they linked Heuermann to the case using a DNA sample taken from a pizza box he threw out and a DNA sample from hair found on burlap used to wrap Waterman's remains. As the court document stated, "It is significant that Defendant Heuermann cannot be excluded from the male hair recovered near the 'bottom of the burlap' utilized to restrain and transport Megan Waterman's naked and deceased body."
Investigators also said in a bail application for Heuermann that they found female hair not belonging to any of the victims in their remains. The DNA sample lifted from the unknown hairs matched DNA believed to belong to Heuermann's wife, who was out of town during the killings, per police.
Authorities have ruled out Ellerup as a suspect, though they believe "it is likely that the burlap, tape, vehicle(s) or other instrumentalities utilized in furtherance of these murders came from Defendant Heuermann's residence, where his wife also resides, or was transferred from his clothing," according to the court docs.
In addition to the DNA samples, police said they found cellphone billing records belonging to Heuermann that appear to correspond to cell site locations for burner phones used to arrange meetings with the three victims.
The bail application read, "Significantly, investigators could find no instance where Heuermann was in a separate location from these other cellphones when such a communication event occurred."
Heuermann remains in police custody after a judge remanded him without bail.
E! News has reached out to Heuermann and Ellerup's attorneys for comment on the divorce filing but hasn't heard back.
(E! and NBC News are both part of the NBCUniversal family.)