Ever since Prime Minister Erdogan stormed off the stage at the World Economic Forum in January 2009 following remarks by Israeli President Shimon Peres, it was clear that Turkish and Israeli relations were entering a turbulent phase.
The rift continued to deepen when Israel refused to allow Turkish Foreign Minister Davutoglu to visit the Gaza strip on an official visit to Israel in September 2009.
In retaliation, Turkey cancelled Israel's participation at a joint international air exercise in October 2009. In January 2010, the diplomatic tensions rocketed when the Israeli Deputy Foreign Minister Daniel Ayalon summoned the Turkish ambassador to protest against an anti-Semitic episode of a popular Turkish television drama.
In a bizarre populist show of superiority, Ayalon sought to insult the Turkish ambassador by placing him on a lower chair and by urging the media to report the lower seating of the ambassador.
Verbal duels between the Netanyahu and Erdogan administrations gave way to subtle signals through cutbacks on defence trade between the two countries, something that has been a major aspect of Turkish Israeli relations.
Since 1990s, Turkey and Israel had enjoyed quiet cooperation on joint military exercises, modernisation of military equipment, intelligence sharing and arms trade in addition to investments in civilian enterprises.
Until last Sunday, there were still strong reasons to believe that Israel and Turkey will continue to enjoy these quiet exchanges but with caution and some downsizing. Things look pretty different now.
Last Sunday's events could have been prevented and Israel could have been saved from a major international public condemnation if it had not chosen to stop the vessels carrying aid to Gaza with a theatrical military operation.
Although the details of exactly what happened is far from clear, the end result is the death of at least nine activists and equal numbers of wounded Israeli soldiers. Israel is still seeking to win a moral and political higher ground by arguing that the flotilla posed a security threat to Israel, if not the entire region, by "supporting" Hamas and other terrorists.
The response of the Turkish government has been extremely strong, yet calculated and carefully ambiguous thus far. Public threats of a major overhaul of Turkish Israeli relations have only been followed by immense efforts at the UN, EU and US levels to force Israel to accept culpability.
However, with the Israeli government continuing to take a hard stance, the statements by various Turkish politicians that things will never be the same again will probably come true. Israel may have just lost its only Muslim ally, and one which is an increasingly ambitious and powerful force in the Middle East.