The yield, physical, and chemical properties of agars from two Philippine red seaweeds, Gracilaria eucheumoides and Gelidiella acerosa, were investigated on a bimonthly basis. The yield of agar from Gracilaria eucheumoides was at a maximum during the early rainy season (May, 29%) and at a minimum during the summer month of March (20%). In Gelidiella acerosa, a peak in agar yield was also recorded in May (21%), with generally higher yields recorded during the rainy than in the dry season. Agar gel strengths fluctuated from 225 to 430 g cm−2 and from 160 to 820 g cm−2 for Gracilaria eucheumoides and Gelidiella acerosa, respectively, and both agars exhibited strongest gels in July. Significant seasonal variations were observed in the gelling and melting temperatures of agar from Gracilaria eucheumoides, but not from Gelidiella acerosa. Sulphate content only varied slightly in agar samples from Gracilaria eucheumoides, while a higher sulphate content was found in Gelidiella acerosa agar during the dry season. Moreover, the sulphate content in G. acerosa agar fluctuated inversely with the 3,6-anhydrogalactose content. A FT-IR analysis showed a fairly constant spectrum for temporal Gracilaria eucheumoides agar while peaks attributed to S–O vibrations intensified in Gelidiella acerosa samples which were recorded to contain high sulphate residues and possess low gel strengths. Diagnosis of the FT-IR spectra in the 1000–400 cm−1 frequency range was also conducted in comparison with agarose and Gracilaria chilensis agar.