Echinometra mathaei is a species complex with its constituent reproductively-isolated species informally called A, B, C and D based on studies done in Okinawa and the Red Sea. Little research has been done on this genus, and to our knowledge no studies have been done on the E. mathaei complex in the Philippines. To help clarify species delineations in the E. mathaei complex, a comparative study was done between two localities in Western Visayas, Philippines: the Taklong Island National Marine Reserve, in Nueva Valencia, Guimaras and Barangay Unidos in Nabas, Aklan. Morphological characteristics (spine color, milled rings, and skin around the peristome) and tubefeet and gonad spicules were observed. Two or possibly three species of Echinometra were found in the two sites based on their morphology and spicules, namely: Echinometra sp. A, Echinometra sp. C, and Echinometra affinity C, which resembles sp. C but differs in the milled rings and gonad spicules. Echinometra sp. C and E. affinity C cannot be distinguished on the basis of field-visible characters, thus the two morphs are referred to as Echinometra VC for the purpose of field surveys. Echinometra VC and Echinometra sp. A exhibited differences in abundance (VC was much more common) and microhabitat (VC was restricted to rocky shores and never observed in coral communities). To study the abundance and distribution of Echinometra VC, 50 m by 2 m belt transects were surveyed along the rocky shores of both sites: two parallel transects (at 0 m and at 0.9 m) and a perpendicular transect (only in Nabas), each with three replicates. The transect data showed that the mean densities for 0 m and 0.9 m in Nabas are significantly higher in Taklong yielding p-values of 0.001 and 0.002, respectively, when analyzed using t-test.Of the two sites, only Nabas showed a significant difference between the mean densities at 0 m and 0.9 m, with the mean density at 0.9 m significantly higher than that of 0 m yielding a p-value of 0.02 when analyzed using two-sample t-test. A Poisson regression on the perpendicular transect data from Nabas showed a trend of increasing Echinometra density with increasing distance from the shore. In the future, DNA barcoding and cross-fertilization studies should be performed in order to confirm the species of Echinometra observed. Many factors can affect the density and distribution of Echinometra, so further studies must be conducted to explain observed differences in their distribution and abundance.