Specialty lowland and upland rices (n = 229) collected from Filipino farmers in 2009–2012 had long-, medium- and short-sized grains. Of these, 108 had intermediate apparent amylose content (AC), 80 had low AC, 26 had high AC and 15 were waxy (mean AC 17.7%). They had mainly intermediate–high gelatinization temperature (GT) by alkali spreading value. High GT was predominant among low-AC specialty rices, instead of low GT. However, the cultivars did not exhibit high milled rice translucency (only 10 had 0–2% chalky grains) and crack (fissure) resistance needed for high head rice recovery required of export quality rice. Only 50 of 225 rices had the 8-base pair deletion at exon 7 of the fragrance gene although many of the rices were aromatic. Alleles of the Waxy (Wx) gene were determined in... selected samples which included the: (1) number of cytosine-thymine repeats [(CT)n] in its untranslated region; (2) G/T single nucleotide polymorphism (SNP) at intron 1; (3) A/C SNP at exon 6; and (4) C/T SNP at exon 10. Combination of the Wx alleles [e.g., 17TAC where: (CT)n is 17, intron 1 SNP is T, exon 6 SNP is A, and exon 10 SNP is C] differentiated the cultivars based on ammonium buffer colorimetric AC. Waxy and low-AC rices were mainly 17TAC. Intermediate-AC rices showed 17GCC, 19GCC and 20GCC Wx alleles combinations while 10GAT and 11GAT were mainly found among high-AC rices. A revision for lowering the AC ranges of apparent amylose types for classification of Philippine rice is proposed based on ammonium buffer AC values verified by differential scanning calorimetry and combination of the Wx alleles: waxy 0.0–2.0%, low AC 10.1–17.0%, intermediate AC 17.1–22.0% and high AC > 22.0%.