"I am certain that he should be looked at as a suspect because of my reaction to his photo and all the other similarities in the cases," Rodriguez, now a grown woman, said in an exclusive interview with "Good Morning America."
"I want closure so badly that I would love for it to be him," she said.
In November 1988, the two girls had been allowed to take their scooters to a nearby store in Hayward, Calif., a trip Michaela had never been allowed to make on her own until that day. As they got ready to leave, they noticed that one of their scooters was missing and split up to find it.
Rodriguez, then also 9 years old, said Michaela was the one to find the missing scooter, which had been moved from where they left it.
"As I bent down to pick up the other scooter I heard screaming," she said.
And as Rodriguez looked up, she got a good look at the kidnapper who had pulled Michaela into the car and sped off. Twenty-one years later when she got a look at Phillip Garrido, and was struck again by his eyes.
Rodgriguez said Michaela has always been in her thoughts, but after Jaycee Dugard was found alive 18 years after her 1991 abduction, she began to have renewed hope that Michaela's kidnapping would be solved -- especially when she saw the car that was impounded from Garrido's house.
That grey Ford sedan, which authorities say was used in Dugard's kidnapping and which is similar to a car seen in the area the day Ilene disappeared, also struck a chord with Rodriguez. So much so that she called Michaela's mother.
"I saw that on the news," she said. "I called Michaela's mother and said 'Oh my God, have you seen this?'"
Rodriguez said she was also startled by the striking resemblence between Michaela and Jaycee Dugard. Seeing photos of Dugard as a child after she was found brought back feelings of guilt, she said, and sadness.
"It's been difficult at times. But I'm thankful I've had the life I have had," she said, adding that she's gone to college, gotten married and had children. "That's something Michaela probably hasn't had."
Authorities found bone fragments on the Garrido property Wednesday and on Thursday, two cadaver dogs "indicated" on the same spot, which will be dug up.
"The first dog, by their description, was very tentative on his indication," said Sgt. J.D. Nelson of the Alameda County Sheriff's Department. "The second dog was more direct and indicating very directly."
Police cautioned that under some circumstances cadaver dogs will give a false positive. On Friday, authorities will begin using archeological dogs, dogs that are able to detect older bones.
It is not yet known whether the bone pieces found this week are animal or human, but a separate bone fragment found in an earlier search as part of the Dugard investigation tested as likely human.
Authorities from several agencies are considering the possibility that Garrido may have been involved in a string of abductions.
"Our investigators immediately started looking into the possibility that the Garridos had some connection," Dublin Polict Lt. Kurtvon Savoye said. "Additionally, we know that based on the Dugard investigation as well as Mr. Garrido's history, these people -- people who commit these offenses -- tend to be predatory and tend to have multiple victims."
Garrido and his wife, Nancy have pleaded not guilty to all charges. Garrido is being held on $30 million bail. Nancy Garrido's attorney has not request bail.
Jaycee Dugard and the two daughters, 11 and 15, that police say Garrido fathered during the young woman's 18-year imprisonment have been kept in seclusion with Dugard's mother, Terry Probyn.
The Associated PABC News Correspondent Brian Rooney and ABC News.com's Meredith Blake contributed to this story.