According to the History of Hisai City, the fifteenth lord of the domain Takayori TODO died in September 1863, and his legitimate son Takayuki TODO was about to succeed him, but he also died in November, and therefore, Takakuni became an adopted son (of either Takayori or Takayuki) in a hurry to succeed to the reigns of the family and to be the sixteenth lord of the domain.
久居市史によると、文久3年（1863年）8月に第15代藩主・藤堂高聴が亡くなり、その嫡男である藤堂高行が継ぐはずだったが10月に死去したため、急遽養子（高聴か高行）となって家督を継ぎ、第16代藩主となる。