Quantitative samples of benthic invertebrates were collected by a core sampler from 4 meso-habitats of a sandy riverbed at relatively slow flowing area of a mountain stream (Takami-gawa Stream, Nara Prefecture). A stretch of ca. 75 m was chosen for the samples collection, where riffle center (RC), riffle edge (RE), center of side pool (SP) and edge of sand bar (EB) were selected for sampling. The first one is a mid-channel habitat, while the others are marginal habitats of the channel. Sampling was carried-out over 5 sampling dates during the years 2008-2009. A total of 19967 individuals of benthic invertebrates, representing 120 taxa were identified. Comparisons using Two-way ANOVA test indicated that total abundance shows significant differences between habitats and seasons, with higher density at RC and in February 2009. Taxon richness exhibited only significant differences between seasons, with also higher value during February 2009. As well, Diversity index (H') showed significant differences between habitats and seasons, with lower values at RC and during May 2008. Dominant taxa such as Paraleptophlebia, Potamanthus, and Zaitzevia showed significant differences between habitats with higher abundance at RC. On the other hand, Oligochaeta exhibited higher abundance at RE. Benthic invertebrates were categorized into 4 groups according to their micro-vertical habitat; epifauna, fugitive fauna, occasional and permanent hyporheos. Occasional hyporheos accounted more than 50% in almost every habitat and sampling month, which was quite different from stony riffles assemblages. The insect larvae of Paraleptophlebia, Potamanthus, and Zaitzevia were predominant occasional hyporheos. This study confirms the suitability of core sampler to collect not only epifauna but also hyporheos in sandy riverbed.