Thanks for your query.Based on the facts that you have posted it appears that you have noticed colour of your semen to be dark yellow in recent times and have been on antibiotics for couple of days without any noticeable change.
The dark colour of the semen is most likely either to be due to less intake of water and infection of either prostate
or seminal vesicle
Please get your semen analysis
done to rule out infection,Utrasound scanning of the abdomen and trans rectal ultrasound
scanning (TRUS)will help to rule out infection of seminal vesicle or prostate .
In the mean while start taking broad spectrum antibiotic like Cefotaxime
twice daily for 3 weeks.
Ensure to drink more water.To keep your urine dilute This will help to change colour of semen .