Aggregatibacter actinomycetemcomitans is a major periodontal pathogen that has several virulence factors such as leukotoxin and cytolethal distending toxin. Although the genes responsible for virulence have been identified, little is known about their regulatory mechanisms. Small RNA (sRNA) has been recognized as an important factor for gene regulation. To identify new regulatory mechanisms via sRNA in A. actinomycetemcomitans HK1651, we performed a systematic search for sRNAs by RNA-seq and identified 90 intergenic region sRNAs and 30 antisense sRNAs. Of the 85 analysable sRNAs, we successfully detected and quantified 70 sRNAs by developing an RT-PCR system, and we identified 17 sRNAs that were differentially expressed during different growth phases. In addition, we found notable intraspecies variation in the sRNA repertoire of A. actinomycetemcomitans, thus suggesting that frequent acquisition or deletion of sRNAs occurred during the evolution of this species. The predicted target genes of the intergenic region sRNAs indicated the possibility of sRNA interaction with several virulence genes including leukotoxin and cytolethal distending toxin. Our results should serve as an important genomic and genetic basis for future studies to fully understand the regulatory network in A. actinomycetemcomitans and provide new insights into the intraspecies variation of the bacterial sRNA repertoire in bacteria.