I'm not entirely sure what you mean.
Story of Seasons is the newest Harvest Moon. lol.
It's developed by the same company as always - MarvelousAQL. It's still a Bokujou Monogatari (Farm Story) game. The only difference is that now XSeed (ie, Marvelous USA) is in charge of the localization. Since Marvelous owns XSeed, the translations are done in-house now and localizations to other countries should be more efficient. At least profit-wise, for them, since they no longer need to go through anyone else.
Natsume used to be in charge of localizations for Bokujou Monogatari games, and they published them under the English title "Harvest Moon". Natsume holds a copyright on the name "Harvest Moon", so XSeed legally couldn't use that name anymore. And apparently Natsume intend to do their own thing in the future under that name. However, Natsume was never the one who developed the games, all they did was translate. The only one they've made in-house was The Lost Valley, which I'm sure you remember most fans found to be lacking.
I don't blame Natsume for holding onto the name. It's really all they have going for them.
tl;dr Because legal issues, Story of Seasons is the new English name for the Harvest Moon series that you know - the one that's always been developed by MarvelousAQL - from 2014 onward.
Future games titled "Harvest Moon" will now be developed directly by Natsume.