Model Kendall, who is currently in Paris for the upcoming Paris Fashion Week, posted a throwback snap of her parents.
The picture showed Kris and Bruce in happier times, and Kendall captioned it with a simple heart emoticon.
Kylie meanwhile left a quote from American writer R.M Drake, and captioned it with a key phrase: "emptiness we created", causing speculation that she believes her parents separation was caused by a disconnect between the pair.
Kris filed the divorce documents on Monday, citing irreconcilable differences, reports Us Weekly.
Kris and Bruce will have joint custody of 17-year-old Kylie, who was the only child listed on the documents, filed at the LA Superior Courthouse. Kendall, 18, was not listed.
According to TMZ, neither Bruce nor Kris will receive spousal support.
The couple's divorce comes almost a year after they announced their separation.
In October last year, the pair told E! News in a joint statement: "We are living separately and we are much happier this way.
"But we will always have much love and respect for each other Even though we are separated, we will always remain best friends and, as always, our family will remain our number one priority."