It's much easier to open the original file for reading, and write a complete new file to another location, and if that all succeeds rename() the new file over the old file:

open INPUT,"<","input.xml" or die $!;
open OUTPUT,">","output.xml.tmp" or die $!;
while (<INPUT>) {
  s/<\/markers>/$database_row<\/markers>/;  # insert $database row bef
+ore marker, if found on this line
  print OUTPUT $_;  # print line to output file
}
close INPUT;
close OUTPUT or die $!;
rename "output.xml.tmp","input.xml";
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If you're doing anything more interesting than your stated problem, it'll be worth it to use a real XML parser instead. I recommend XML::Twig.