There are conflicting hypotheses on the origin of the name "Siddi". One theory is that the word was a term of respect in North Africa, similar to the word "sahib" in modern India and Pakistan. A second theory is that the term "Siddi" is derived from the title borne by the captains of the Arab vessels that first brought Siddi settlers to India. These captains were known as "Sayyid".

Similarly, another term for Siddis, "habshi" (from "Al-Habsh", the Arabic term for Abyssinia), is held to be derived from the common name for the captains of the Ethiopian/Abyssinian ships that also first delivered Siddi slaves to the subcontinent. The term eventually came to be applied to other Africans and not only to emancipated Siddis. In time, it came to be used to refer to their descendants as well. It is sometimes pronounced "Hafsi" and is considered an insult.

Siddis are also sometimes referred to as Afro-Indians. Siddis were referred to as "Zanji" by Arabs; in China, various transcriptions of this Arabic word were used, including "Xinji" (辛吉) and "Jinzhi" (津芝).

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ઓટોસોમલ રંગસૂત્ર (Autosomal DNA)