Koyuki and Dororo are both partners and good friends, since Koyuki's reason to come to Tokyo was to help Dororo reunite with his comrades, only to find that Dororo was most forgotten by the platoon, especially his childhood friend, Keroro. Koyuki first met Dororo (Zeroro back then) while still living in her ninja village, and there, Dororo learned the beauty of Earth and its nature, explaining his reluctant attitude towards the more Earth-threatening plans of Keroro. They live together in Koyuki's cottage in the forest (anime) / next door to the Hinata's (manga). Koyuki and Dororo have a very strong sibling-like bond, they obviously get along better with each other than Natsumi and the other platoon members.
Koyuki and Shizune have a mother-daughter relationship. Being the Shizune's adopted daughter, They manage to have close bond. Shizune is aslo her sensei in her ninja training despite Koyuki knowing the most basic ninja skills like charka control, and weapons.
Koyuki and Aqua have a sister-like relationship. Being the second youngest on the team, Aqua looks out for Koyuki when very some goes wrong on a mission and makes sure she is okay.
Similar to her relationship with Aqua, They are very close, since Sakura is Koyuki's teacher in medical jutsu along with Shizune, who is her other teacher and adoptive mother.