It was one of the more bizarre episodes in the refugee crisis. Seehofer, leader of the Christian Social Union (CSU) - the Bavarian sister party to Merkel's conservative Christian Democratic Union (CDU) - sent a letter to the Chancellor's office in Berlin threatening to sue the government over its refugee policy.
In the letter, Seehofer demanded that the government show it was taking steps to reduce the number of refugees arriving in the country and to set an upper limit of 200,000 on the new arrivals whom Germany would accept yearly.
If the government failed to take the steps to reduce the influx, the Bavarian Minister-President threatened in the letter to go to the constitutional court, the highest legal authority in the land.
With Bavaria on the front line of the crisis - its border with Austria is the main crossing point for new arrivals reaching Germany - Seehofer had been under pressure for months from hardliners in the CSU and public opinion to act.
But the threat to sue the government which his own party was a part of left many scratching their heads, and led to scorn from the north German media, which loves to portray Bavaria as a state with more money than sense.
Some commentators went as far as to suggest that the letter was part of an attempt to topple the Chancellor and take her place.
Merkel herself refused to respond publicly to the letter, saying only that “one answers letters rather than talking about them.”
Clearly, Merkel has had a lot of letters to respond to.
On Monday, almost three months after he popped his original correspondence in the post box, Seehofer finally received a reply.
In a three-page response Merkel wrote that Seehofer's accusation in his letter that the government was doing nothing to reduce the refugee numbers was completely unfounded, according to Munich daily the Süddeutsche Zeitung (SZ), which has seen the letter.
Mentioning the donor conference which took place at the start of February in London, at which Germany pledged €2.3 billion in aid to refugee camps in the countries neighbouring Syria, Merkel says the government has been fighting the causes of the refugee influx.
She then describes how the EU's treaty with Turkey, agreed upon in the middle of March, which allows for Greece to send migrants back to Turkey, is further evidence that Berlin is working to reduce the number of arrivals.
With all this work, the Chancellor appears to have lost track of time, failing to notice that these steps took place after Seehofer sent his original letter.
The Bavarian government, though, senses a more cynical motive at work, suggesting to the SZ that Merkel deliberately waited until refugee numbers dropped before writing a response.
Whereas at the high point of the crisis as many as 10,000 migrants were arriving daily at the Bavarian border, the numbers have now dropped to a less than a hundred per day.
CSU insiders also complain that the letter did not address their central arguments and warn that legal action is still very much on the table.
'Haven't yet read it'
On Monday, the Bavarian leader was at pains to show that he was also in no rush to rip open the Chancellor's envelope.
He hadn't yet read the letter, he told the SZ, adding that he would do so in the coming days.
"It's not the case that all hell breaks loose here whenever a letter arrives from the Chancellery," he insisted.
The letter will be read "in complete calm", before Seehofer sits down to put ink to paper on the next exchange with his new pen pal.
But Merkel shouldn't expect to find a letter with a Bavarian postmark in her inbox just yet.
When the weather in the Mediterranean improves and the sun comes out - meaning that more people may set off in boats towards Europe - Seehofer might be more inclined to sit down at his writing desk, insiders suggest.