Although you sometimes see people getting muddled in Methods sections, nobody sequences rRNA in phylogenetic studies these days. They PCR from a DNA (not RNA) template and sequence that- it is DNA from start to finish. Not so at the start of the molecular phylogenetics era when rRNA sequences actually came directly from RNA extracted from cells. Giovanni is spot on though, and rRNA should be treated as a name for the product of the gene we are talking about, e.g. "I sequenced single stranded binding protein" usually doesn't mean you did anything with a protein, rather sequenced the gene and predicted the amino acids.
"18S ribosomal RNA" is the name of the product of the gene. You should take it as a name, as if it were the name of a protein. The AY742884 entry identifies the DNA sequence that encodes for the 18S rRNA.