Most big temples in the South are run by a state department or a devaswom board. Here is each one with its official website and the temples on Temple Yatra that it manages.
Andhra Pradesh
AP Endowments Department
Over 21,000 templesunder this department (official figures, approximate)
Under the A.P. Charitable & Hindu Religious Institutions & Endowments Act, 1987. Major devasthanams: Srisailam, Simhachalam, Annavaram, Vijayawada Kanaka Durga, Srikalahasti, Kanipakam, Dwaraka Tirumala.
Andhra Pradesh
Tirumala Tirupati Devasthanams (TTD)
About 65 templesunder this department (official figures, approximate)
Independent trust board for Tirumala and its local and outstation temples.
Telangana
Telangana Endowments Department
Thousands of templesunder this department (official figures, approximate)
Commissionerate of Endowments, Hyderabad. Major temples: Yadadri, Bhadrachalam, Vemulawada, Basara, Keesaragutta, Komuravelli.
Karnataka
Karnataka Muzrai Department (HRI & CE)
About 34,500 templesunder this department (official figures, approximate)
Hindu Religious Institutions & Charitable Endowments Department. Its Integrated Temple Management System (ITMS) lists all Muzrai temples with sevas and booking.
Tamil Nadu
Tamil Nadu HR&CE Department
About 44,000 templesunder this department (official figures, approximate)
Hindu Religious & Charitable Endowments Department, Chennai. Publishes the list of temples district-wise on its website.
Kerala
Travancore Devaswom Board
About 1,250 templesunder this department (official figures, approximate)
Southern Kerala, including Sabarimala.
Kerala
Cochin Devaswom Board
About 400 templesunder this department (official figures, approximate)
Central Kerala (Ernakulam, Thrissur, Palakkad); headquarters in Thrissur.
Kerala
Malabar Devaswom Board
About 1,340 templesunder this department (official figures, approximate)
North Kerala (Malabar); headquarters in Kozhikode.
Kerala
Guruvayur Devaswom
12 templesunder this department (official figures, approximate)
Guruvayur Sri Krishna temple and its associated temples.