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I'm writing a story, it's not focused on romance, but that's an important part as well. The point is that I have two characters and I ended up ("accidentally") seeing chemistry between them, they have a good dynamic. With that, I really want to know how to develop a romance between them without being obvious.

How can I make the chemistry be perceived without giving evidence that they will be a couple in the future? I want to do it in a way that the reader can see the chemistry and the romantic potential that they have, so that they come and ship the couple without having any certainty that they will be canon someday.

I want the reader to have the impression that it will probably never happen, but that he still has a tiny spark of hope. As if thinking, "I know it will probably never happen, but I ship it anyway.", Anyway, what I meant by that, is that the idea is to make the reader think that he is deluding himself, and at the same time not (I think it's kind of confusing, sorry). Exemplifying would be like Romanogers (Marvel), Finrey (Star Wars), Stydia (Teen Wolf), or even Scalia in 6A of Teen Wolf.

So I ask again, how to develop a romance that is not obvious? How can chemistry be perceived without giving evidence that they will be a couple in the future? The funniest thing is that, unintentionally, I ended up shipping them, so I'm hoping they'll be together!

I think it, sadly, depends on the genders of your characters. If it's a m/f couple people are much more likely to notice the chemistry and start shipping them faster and have more hope that they'll actually get together. With a m/m or m/f ship you're much more likely to pass under the radar and have the chemistry chalked up to just being good friends or seeing each other like siblings, so you may have to be more aggressive to get a lot of readers to go 'oh this is romantic!' But on the other hand it will be a lot easier to pass unnoticed if you decide you want it to hit readers unexpectedly.

That being said, the easiest way to get people to think about characters being romantically involved is to showcase that chemistry. Have them spend time together, banter, bounce ideas off each other and joke around. If there's an obvious or major barrier for why they can't/won't be together that will provide the 'oh they'll never be together' since this isn't a romance-focused story (I found a list of examples of barriers here, but there's lots of others if you google something like 'romance barriers/conflicts'. It's for romance novels, but it's really all a case of how much time you spend on the romance. In this case you don't need to dwell on it, I don't think.)

How can chemistry be perceived without giving evidence that they will be a couple in the future?

You can make the chemistry perceptible without going over the top, but then you need a barrier between them, something the characters feel will not change and will not allow them to be together.

One of them is happily married with no intent of cheating; perhaps both of them are. But later you (the author) kill the spouse in the way, through no intent of either character.

Or one of them is homosexual, and believes they are homosexual, but eventually because they realize they are in love and fantasizing about the other, discovers they are bisexual.

Or vice versa, if you have a homosexual relationship. I know a woman (a platonic friend of mine for 20 years) that thought she was heterosexual, due to an upbringing in a religious church-going household. She did not realize she was homosexual until she was in her mid-twenties. (This was in the early 1980's before the Internet was common.)

You can make the barrier legal: It is common in military outfits that an officer cannot have intimate relationships with subordinates, this can be a court-martial offense, and sexual harassment even if the subordinate consents: but free consent cannot be a certainty when the superior officer has influence over the career of the subordinate. And that is real life, in fiction you can make the requirements that much harder, e.g. make it a prison offense with a mandatory five year minimum.

Other legal barriers can exist (and have) over race, religion, citizenship, and sexual orientation (until recently homosexual sex was illegal in many jurisdictions within the USA, and still is in many jurisdictions throughout the world, even if anal or oral sex IS legal between a man and a woman).

IN ANY CASE, what you need is to add in a huge barrier, a stumbling block. It can be psychological, or marital, or incompatible sexual orientation, or a legal prohibition, or perhaps just a physical barrier of vast distance: they have obvious chemistry, but are separated by a distance it is very unlikely they will overcome.

Make the barrier as obvious and compelling as the chemistry; perhaps even more compelling. Perhaps there are multiple barriers. Then someday, all barriers evaporate, and when they realize this, they pursue their chemistry and consummate their romantic relationship.