In this paper we shall discuss three issues related to the so-called zero initials in the Menggu Ziyun 蒙古字韻 (MGZY). The first and the main issue involves the four initial letters y, a, L, and K, the second one involves the three initial-less syllables U, Pm, and O, and the third one involves the initial letter w. Our analyses of the zero initials reveal the complex relationship between the phonological system, the phonetic values, and the hP’ags-pa spellings. We show that the distinction of the four zero initial letters is based on the divisions of the Song-Yuan rhyme tables. But their phonetic differences are not clearly reflected in the hP’ags-pa spellings. This phenomenon indicates the discrepancy between the inherited phonology and the phonetic values of the living language. The three initial-less letters also demonstrate the same discrepancy. The initial letter w illustrates the inconsistency between the intrinsic value of the letter and the actual phonetic value it intends to transcribe. There is no question that the phonetic values contained in the hP’ags-pa spellings are valuable. But our analyses demonstrate that it would be a mistake to think that the face values of the hP’ags-pa letters accurately reveal the phonetics of the MGZY phonology.