Short answer. The court authorized to hear family cases, if one exists in your area; otherwise the regional trial court or its equivalent sitting where either spouse resides. Jurisdiction is exercised upon proof of notice to the other spouse, so notice is not a formality to be dealt with later.
What the law says
Jurisdiction over the petition shall, upon proof of notice to the other spouse, be exercised by the proper court authorized to hear family cases, if one exists, or in the regional trial court or its equivalent sitting in the place where either of the spouses resides.
Family Code, Article 241 — Jurisdiction Over the Petition. Read the full provision →
A first choice and a fallback
The article sets an order rather than a menu. Where a court authorised to hear family cases exists, that is the proper forum. Where none exists in the place concerned, the petition goes to the regional trial court or its equivalent. The fallback is not an alternative you may prefer for convenience; it applies when the first option is unavailable. So the practical first step is to find out what courts sit in the relevant place and whether any of them is designated to hear family cases.
Either spouse's residence will do
The place is fixed by residence, and the article is generous about whose: the place where either of the spouses resides. That is deliberate, because these petitions arise precisely where the spouses are separated in fact or one has abandoned the other, and requiring the petitioner to follow the absent spouse would defeat the remedy. Your own residence is therefore a sufficient basis. Note that it is residence, not the location of the property — a couple living in one province may petition there over land held in another.
Notice is built into jurisdiction
The most consequential words are the ones in the middle: jurisdiction is exercised upon proof of notice to the other spouse. Notice is not a procedural courtesy that can be sorted out as the case moves along; the court's power to act on the petition is conditioned on proof that the other spouse was notified. Even a summary proceeding designed to deal with a refusing or absent spouse does not proceed behind that spouse's back. Expect the court to look at your proof of notice before it looks at anything else.
Prepare the notice problem first
If your spouse has disappeared, the hardest part of this petition is the part the article makes jurisdictional, so start with it. Assemble his last known address and the record of your efforts to locate him — messages, letters returned, enquiries with relatives, employers or neighbours — and keep that record as you go rather than reconstructing it afterwards. Bring it, with the marriage certificate and the documents on the property and the proposed transaction, when you consult a lawyer. Where and how notice can properly be given is the question that shapes the timetable.