You may also use the rule's number (--line-numbers):
iptables -L INPUT --line-numbers
Example output :
Chain INPUT (policy ACCEPT)
num target prot opt source destination
1 ACCEPT udp -- anywhere anywhere udp dpt:domain
2 ACCEPT tcp -- anywhere anywhere tcp dpt:domain
3 ACCEPT udp -- anywhere anywhere udp dpt:bootps
4 ACCEPT tcp -- anywhere anywhere tcp dpt:bootps
So if you would like to delete second rule :
iptables -D INPUT 2
If you use(d) a specific table (eg nat), you have to add it to the delete command (thx to @ThorSummoner for the comment)
sudo iptables -t nat -D PREROUTING 1