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Hello.
Were EC2 and RDS originally running in the same subnet?
Looking at the configuration diagram, the subnets are separated and communication occurs between AZs.
Communication between AZs will result in a difference in performance compared to communication within the same AZ.
You can perform a simple benchmark test by following the steps in the document below, which may be helpful.
https://repost.aws/knowledge-center/network-throughput-benchmark-linux-ec2
Additionally, IO performance may be improved somewhat by changing the RDS storage settings.
https://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/CHAP_Storage.html
@Riku_Kobayashi So the first infrastructure was all in one subdomain. I tried to move the new one to one Azs to eu-cental-1b but it didn't help. There are still EC2 and rds in different subdomains. Can the fact that they are in private networks and EC2 uses a NAT gateway to communicate with the Internet have an impact on latency?
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Since NAT Gateway is not used for communication within the VPC, I don't think it is related to communication latency between EC2 and RDS. I suspect that latency is occurring in communication between subnets in different AZs.